Morgan Stanley Institutional Fund Trust N-CSR Certified annual shareholder report (management investment company)

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM N-CSR

CERTIFIED SHAREHOLDER REPORT OF REGISTERED

MANAGEMENT INVESTMENT COMPANIES

Investment Company Act file number: 811-03980

Morgan Stanley Institutional Fund Trust

(Exact name of registrant as specified in charter)

522 Fifth Avenue, New York, New York	10036
(Address of principal executive offices)	(Zip code)

John H. Gernon

522 Fifth Avenue, New York, New York 10036

(Name and address of agent for service)

Registrant's telephone number, including area code: 212-296-0289

Date of fiscal year end: September 30,

Date of reporting period: September 30, 2020

Item 1 - Report to Shareholders

INVESTMENT MANAGEMENT

Morgan Stanley Institutional Fund Trust

Core Plus Fixed Income Portfolio

Annual Report

September 30, 2020

Beginning on January 1, 2021, as permitted by regulations adopted by the Securities and Exchange Commission ("SEC"), paper copies of the Fund's Annual and Semi-Annual Reports to Shareholders ("Shareholder Reports") will no longer be sent by mail, unless you specifically request paper copies of the Shareholder Reports from the Fund or from your financial intermediary, such as a broker-dealer or a bank. Instead, the Shareholder Reports will be made available on the Fund's website, https://www.morganstanley.com/im/shareholderreports and you will be notified by mail each time a Shareholder Report is posted and provided with a website link to access the Shareholder Report. If you already elected to receive Shareholder Reports electronically, you will not be affected by this change and you need not take any action. You may elect to receive Shareholder Reports and other communications from the Fund electronically anytime by contacting your financial intermediary or, if you are a direct investor, please follow the instructions on the envelope.

Beginning on January 1, 2019, you may elect to receive all future Shareholder Reports in paper free of charge. If you invest through a financial intermediary, you can contact your financial intermediary to request that you continue to receive paper copies of your Shareholder Reports. If you invest directly with the Fund, please follow the instructions on the envelope to let the Fund know you wish to continue receiving paper copies of your Shareholder Reports. Your election to receive Shareholder Reports in paper will apply to all funds held in your account if you invest through your financial intermediary or all funds held with the fund complex if you invest directly with a fund.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Table of Contents

Shareholders' Letter	2
Expense Example	3
Investment Overview	4
Portfolio of Investments	6
Statement of Assets and Liabilities	20
Statement of Operations	22
Statements of Changes in Net Assets	23
Financial Highlights	25
Notes to Financial Statements	30
Report of Independent Registered Public Accounting Firm	42
Investment Advisory Agreement Approval	43
Liquidity Risk Management Program	45
Federal Tax Notice	46
Privacy Notice	47
Trustee and Officer Information	49

This report is authorized for distribution only when preceded or accompanied by a prospectus or summary prospectus of the applicable Fund of the Morgan Stanley Institutional Fund Trust. To receive a prospectus and/or statement of additional information ("SAI"), which contains more complete information such as investment objectives, charges, expenses, policies for voting proxies, risk considerations and describes in detail each of the Fund's investment policies to the prospective investor, please call toll free 1 (800) 548-7786. Please read the prospectuses carefully before you invest or send money.

Additionally, you can access information about the Fund, including performance, characteristics and investment team commentary, through Morgan Stanley Investment Management's website: www.morganstanley.com/im/shareholderreports.

Market forecasts provided in this report may not necessarily come to pass. There is no guarantee that any sectors mentioned will continue to perform as discussed herein or that securities in such sectors will be held by the Fund in the future. There is no assurance that a fund will achieve its investment objective. Funds are subject to market risk, which is the possibility that market values of securities owned by the Fund will decline and, therefore, the value of the Fund's shares may be less than what you paid for them. Accordingly, you can lose money investing in this Fund. Please see the prospectus for more complete information on investment risks.

1

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Shareholders' Letter (unaudited)

Dear Shareholders,

We are pleased to provide this Annual Report, in which you will learn how your investment in Core Plus Fixed Income Portfolio (the "Fund") performed during the latest twelve-month period.

Morgan Stanley Investment Management is a client-centric, investor-led organization. Our global presence, intellectual capital, and breadth of products and services enable us to partner with investors to meet the evolving challenges of today's financial markets. We aim to deliver superior investment service and to empower our clients to make the informed decisions that help them reach their investment goals.

As always, we thank you for selecting Morgan Stanley Investment Management, and look forward to working with you in the months and years ahead.

Sincerely,

John H. Gernon
President and Principal Executive Officer

October 2020

2

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Expense Example (unaudited)

Core Plus Fixed Income Portfolio

As a shareholder of the Fund, you may incur two types of costs: (1) transactional costs, including sales charge (loads) on purchase payments; and (2) ongoing costs, which may include advisory fees, administration fees, distribution and shareholder services fees; and other Fund expenses. This example is intended to help you understand your ongoing costs (in dollars) of investing in the Fund and to compare these costs with the ongoing costs of investing in other mutual funds.

This example is based on an investment of $1,000 invested at the beginning of the six-month period ended September 30, 2020 and held for the entire six-month period.

Actual Expenses

The table below provides information about actual account values and actual expenses. You may use the information in this table, together with the amount you invested, to estimate the expenses that you paid over the period. Simply divide your account value by $1,000 (for example, an $8,600 account value divided by $1,000 = 8.6), then multiply the result by the number in the table under the heading entitled "Actual Expenses Paid During Period" to estimate the expenses you paid on your account during this period.

Hypothetical Example for Comparison Purposes

The table below provides information about hypothetical account values and hypothetical expenses based on the Fund's actual expense ratio and an assumed rate of return of 5% per year before expenses, which is not the Fund's actual return. The hypothetical account values and expenses may not be used to estimate the actual ending account balance or expenses you paid for the period. You may use this information to compare the ongoing costs of investing in the Fund and other funds. To do so, compare this 5% hypothetical example with the 5% hypothetical examples that appear in the shareholder reports of the other funds.

Please note that the expenses shown in the table are meant to highlight your ongoing costs only and do not reflect any transactional costs, such as sales charges (loads, if applicable). Therefore, the information for each class in the table is useful in comparing ongoing costs only, and will not help you determine the relative total costs of owning different funds. In addition, if these transactional costs were included, your costs would have been higher.

	Beginning Account Value 4/1/20		Actual Ending Account Value 9/30/20		Hypothetical Ending Account Value		Actual Expenses Paid During Period*		Hypothetical Expenses Paid During Period*		Net Expense Ratio During Period**
Core Plus Fixed Income Portfolio Class I	$	1,000.00	$	1,081.30	$	1,023.00	$	2.08	$	2.02		0.40	%
Core Plus Fixed Income Portfolio Class A		1,000.00		1,079.30		1,021.25		3.90		3.79		0.75
Core Plus Fixed Income Portfolio Class L		1,000.00		1,077.80		1,020.00		5.19		5.05		1.00
Core Plus Fixed Income Portfolio Class C		1,000.00		1,075.30		1,017.80		7.47		7.26		1.44
Core Plus Fixed Income Portfolio Class IS		1,000.00		1,080.60		1,023.25		1.82		1.77		0.35

*  Expenses are calculated using each Fund Class' annualized net expense ratio (as disclosed), multiplied by the average account value over the period and multiplied by 183/366 (to reflect the most recent one-half year period).

**  Annualized.

3

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Overview (unaudited)

Core Plus Fixed Income Portfolio

The Fund seeks above-average total return over a market cycle of three to five years.

Performance

For the fiscal year ended September 30, 2020, the Fund's Class I shares had a total return based on net asset value and reinvestment of distributions per share of 6.27%, net of fees. The Fund's Class I shares underperformed against the Fund's benchmark, the Bloomberg Barclays U.S. Aggregate Index (the "Index"), which returned 6.98%.

Factors Affecting Performance

•  Government bond yields declined significantly over the period, particularly in the first quarter of 2020, in the U.S. and throughout the world. This slightly hurt relative performance because the Fund had a short duration position in the U.S. as rates fell. The portfolio had a long duration position in both emerging markets and non-U.S. developed markets, however, which helped relative performance as rates fell in those regions.

•  The Fund's exposure to Treasury inflation-protected securities (TIPS) hurt relative performance during the beginning of the first quarter 2020, and the position was subsequently closed out as inflation breakevens began to narrow.

•  Over the period, the portfolio's overweight to both investment grade and high yield corporate bonds contributed to relative performance given the significant rally during the second and third quarters of 2020.

•  The Fund was hurt by its exposure to emerging market debt, which lagged the initial recovery seen in the second quarter of 2020 after the market sell-off caused by the coronavirus pandemic.

•  Overall securitized positioning detracted from relative performance during the period, particularly in areas that were disproportionately affected by the lockdowns caused by the coronavirus. Exposure in areas such as asset-backed securities (ABS) and non-agency commercial mortgage-backed securities (CMBS) were the largest detractors in the sector. However, positioning in non-agency and agency residential mortgage-backed securities (RMBS) contributed to relative performance as these sub-sectors rallied significantly in the second and third quarters of 2020.

Management Strategies

•  We see little risk of government bond yields rising meaningfully anytime soon. Recent rises in yields during September 2020 appear to have been more technical in nature and/or related to shifting probabilities of who will be elected the next U.S. president. However, further declines in yields also seem unlikely, given that most central banks have now cut interest rates to as low as they feel comfortable doing. Nonetheless, further cuts and other policy innovations could still happen if there is a turn for the worse, so there is still a case, we believe, for owning high-quality government bonds as a hedge against further stress, even if much less than normal.

•  We remain constructive on corporate credit. Although we continue to hold a positive and upbeat view with regard to the evolution of the economy and credit spreads, risks remain. Rising infection rates, leading to larger and more aggressive lockdowns, could easily slow economies and upend our views. We do not think this is likely, as all governments seem to be adopting more selective, targeted lockdowns to deal with local issues. As long as local issues do not spread and/or hospitalization rates/mortality rates do not climb too much, economies should be fine. Vaccines continue to be the linchpin of a broader solution to get sectors of the economy like travel, leisure and entertainment back to semi-normal, thus allowing national incomes to return back to pre-COVID-19 levels.

•  In the securitized assets sector, we still have a positive fundamental credit outlook for U.S. residential and consumer credit conditions given various government support programs that have been put in place in response to the coronavirus pandemic. Additionally, mortgage fundamental performance has been generally positive so far, as loan delinquencies and forbearance requests continue to decline, and remain much lower than most market forecasts given current unemployment forecasts. National home prices are up almost 5% over the past year, fueled by record low mortgage rates and historically low housing supply.ⁱ We expect the U.S. housing market to remain stable and non-agency RMBS to continue to perform relatively well from a credit perspective in the near future.

ⁱ  Source: S&P CoreLogic Case Shiller U.S. National Home Price Index, September 29, 2020. The index measures U.S. residential real estate prices, tracking changes in the value of residential real estate nationally.

4

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Overview (unaudited) (cont'd)

Core Plus Fixed Income Portfolio

•  We remain cautiously optimistic on emerging market debt in the near term on the back of continued global monetary and fiscal policy accommodation. A continued rebound in China growth, to the extent that spills over to the global economy, should also provide a further boost to risky assets, as well as any positive developments on coronavirus treatments and vaccines. On the other hand, our relatively constructive view on emerging market assets in the near term is tempered by less compelling valuations, increased volatility due to the upcoming U.S. presidential election, and some setbacks on the fight against the pandemic, as evidenced in increasing case counts in Europe and stricter lockdown measures imposed in several countries.

*  Minimum Investment

In accordance with SEC regulations, the Fund's performance shown assumes that all recurring fees (including management fees) were deducted and all dividends and distributions were reinvested. The performance of Class A, Class L, Class C and Class IS shares will vary from the performance of Class I shares based upon their different inception dates and will be negatively impacted by additional fees assessed to those classes (where applicable).

Performance Compared to the Bloomberg Barclays U.S. Aggregate Index⁽¹⁾ and the Lipper Core Plus Bond Funds Index⁽²⁾

	Period Ended September 30, 2020 Total Returns(3)
				Average Annual
	One Year			Five Years			Ten Years			Since Inception(9)
Fund — Class I Shares w/o sales charges(4)		6.27	%		6.73	%		5.61	%		7.17	%
Fund — Class A Shares w/o sales charges(5)		5.91			6.35			5.27			4.95
Fund — Class A Shares with maximum 3.25% sales charges(5)		2.46			5.66			4.93			4.81
Fund — Class L Shares w/o sales charges(6)		5.63			6.08			—			4.93
Fund — Class C Shares w/o sales charges(7)		5.16			5.58			—			4.74
Fund — Class C Shares with maximum 1.00% deferred sales charges(7)		4.16			5.58			—			4.74
Fund — Class IS Shares w/o sales charges(8)		6.24			—			—			7.67
Bloomberg Barclays U.S. Aggregate Index		6.98			4.18			3.64			6.90
Lipper Core Plus Bond Funds Index		6.91			4.68			4.19			—

Performance data quoted represents past performance, which is no guarantee of future results, and current performance may be lower or higher than the figures shown. Performance assumes that all dividends and distributions, if any, were reinvested. For the most recent month-end performance figures, please visit www.morganstanley.com/im/shareholderreports. Investment returns and principal value will fluctuate so that Fund shares, when redeemed, may be worth more or less than their original cost. Total returns do not reflect the deduction of taxes that a shareholder would pay on Fund distributions or the redemption of Fund shares. Performance of share classes will vary due to differences in sales charges and expenses.

⁽¹⁾  The Bloomberg Barclays U.S. Aggregate Index tracks the performance of U.S. government agency and Treasury securities, investment-grade corporate debt securities, agency mortgage-backed securities, asset-backed securities and commercial mortgage-backed securities. The Index is unmanaged and its returns do not include any sales charges or fees. Such costs would lower performance. It is not possible to invest directly in an index.

⁽²⁾  The Lipper Core Plus Bond Funds Index is an equally weighted performance index of the largest qualifying funds (based on net assets) in the Lipper Core Plus Bond Funds classification. The Index, which is adjusted for capital gains distributions and income dividends, is unmanaged and should not be considered an investment. There are currently 30 funds represented in this Index. As of the date of this report, the Fund was in the Lipper Core Plus Bond Funds classification.

⁽³⁾  Total returns for the Fund reflect expenses waived and/or reimbursed, if applicable, by the Adviser. Without such waivers and/or reimbursements, total returns would have been lower.

⁽⁴⁾  Commenced operations on November 14, 1984.

⁽⁵⁾  Commenced offering on November 7, 1996.

⁽⁶⁾  Commenced offering on April 27, 2012.

⁽⁷⁾  Commenced offering on April 30, 2015.

⁽⁸⁾  Commenced offering on June 15, 2018.

⁽⁹⁾  For comparative purposes, average annual since inception returns listed for the Indexes refer to the inception date of Class I of the Fund, not the inception of the Indexes.

5

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments

Core Plus Fixed Income Portfolio

	Face Amount (000)		Value (000)
Fixed Income Securities (97.8%)
Agency Adjustable Rate Mortgage (0.0%)
Federal Home Loan Mortgage Corporation, Conventional Pools: 12 Month USD LIBOR + 1.62%, 3.00%, 7/1/45	$	52	$	54
Agency Fixed Rate Mortgages (23.0%)
Federal Home Loan Mortgage Corporation,
Conventional Pools:
2.50%, 11/1/49		1,532		1,609
3.00%, 11/1/49 - 12/1/49		2,004		2,071
3.50%, 8/1/49		818		845
4.00%, 4/1/49 - 11/1/49		3,097		3,260
4.50%, 2/1/49		1,255		1,357
Gold Pools:
3.00%, 3/1/47 - 6/1/49		2,734		2,873
3.50%, 1/1/44 - 4/1/49		1,482		1,609
4.00%, 6/1/44 - 1/1/48		938		1,016
5.41%, 7/1/37 - 8/1/37		20		21
5.44%, 1/1/37 - 2/1/38		50		55
5.46%, 5/1/37 - 1/1/38		52		57
5.48%, 8/1/37 - 10/1/37		36		41
5.50%, 8/1/37 - 4/1/38		72		81
5.52%, 10/1/37		5		6
5.62%, 12/1/36 - 8/1/37		59		66
6.00%, 10/1/36 - 8/1/38		97		111
6.50%, 12/1/25 - 8/1/33		74		84
7.00%, 6/1/28 - 11/1/31		31		31
Federal National Mortgage Association,
Conventional Pools:
2.50%, 10/1/49 - 2/1/50		3,642		3,773
3.00%, 6/1/40 - 1/1/50		11,095		11,516
3.50%, 8/1/45 - 11/1/49		8,718		9,205
4.00%, 11/1/41 - 9/1/49		6,744		7,271
4.50%, 3/1/41 - 8/1/49		2,907		3,170
5.00%, 3/1/41		163		188
5.50%, 6/1/35 - 1/1/37		49		58
5.62%, 12/1/36		31		33
6.50%, 4/1/24 - 1/1/34		673		761
7.00%, 5/1/24 - 12/1/33		120		132
9.50%, 4/1/30		48		54
October TBA:
2.00%, 10/1/50 (a)		19,025		19,672
2.50%, 10/1/50 (a)		30,600		32,100
3.00%, 10/1/35 - 10/1/50(a)		62,460		65,440
3.50%, 10/1/50 (a)		24,000		25,306
Government National Mortgage Association,
Various Pools:
3.50%, 11/20/40 - 7/20/49		1,868		1,985
4.00%, 8/20/41 - 11/20/49		8,746		9,310
4.50%, 4/20/49 - 7/20/49		1,425		1,509
5.00%, 12/20/48 - 2/20/49		201		217
6.50%, 5/15/40		419		499
				207,392

	Face Amount (000)		Value (000)
Asset-Backed Securities (12.2%)
Aaset Trust,
3.84%, 5/15/39 (b)	$	443	$	418
Accredited Mortgage Loan Trust,
1 Month USD LIBOR + 0.60%, 0.75%, 4/25/34 (c)		686		677
Ajax Mortgage Loan Trust,
1.70%, 5/25/59 (b)		2,583		2,591
American Homes 4 Rent Trust,
6.07%, 10/17/52 (b)		601		674
AMSR 2019-SFR1 Trust,
2.77%, 1/19/39 (b)		3,100		3,293
Aqua Finance Trust,
3.47%, 7/16/40 (b)		900		930
Avant Loans Funding Trust,
4.65%, 4/15/26 (b)		850		832
5.00%, 11/17/25 (b)		525		527
BCMSC Trust,
7.51%, 1/15/29 (c)		1,474		1,422
Blackbird Capital Aircraft Lease Securitization Ltd.,
5.68%, 12/16/41 (b)		771		542
Cascade Funding Mortgage Trust,
5.60%, 4/25/30 (b)(c)		1,000		1,054
7.30%, 4/25/30 (b)(c)		2,000		2,115
Cascade MH Asset Trust,
4.00%, 11/25/44 (b)(c)		1,510		1,559
CFMT 2020-HB3 LLC,
6.28%, 5/25/30 (b)(c)		1,100		1,111
Conn's Receivables Funding LLC,
3.62%, 6/17/24 (b)		1,000		989
Consumer Loan Underlying Bond Credit Trust,
4.41%, 10/15/26 (b)		2,000		1,936
4.66%, 7/15/26 (b)		1,000		973
5.21%, 7/15/25 (b)		1,136		1,127
ContiMortgage Home Equity Loan Trust,
8.10%, 8/15/25		20		16
Diamond Resorts Owner Trust,
4.02%, 2/20/32 (b)		1,226		1,206
Fair Square Issuance Trust,
2.90%, 9/20/24 (b)		900		901
Fairstone Financial Issuance Trust I,
3.95%, 3/21/33 (b)	CAD	600		451
Falcon Aerospace Ltd.,
3.60%, 9/15/39 (b)	$	962		887
FCI Funding 2019-1 LLC,
3.63%, 2/18/31 (b)		362		368
Foundation Finance Trust,
3.86%, 11/15/34 (b)		592		611
FREED ABS Trust,
3.19%, 11/18/26 (b)		2,000		1,987
3.87%, 6/18/26 (b)		800		802
4.52%, 6/18/27 (b)		1,004		1,016
4.61%, 10/20/25 (b)		969		972

The accompanying notes are an integral part of the financial statements.
6

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Core Plus Fixed Income Portfolio

	Face Amount (000)		Value (000)
Asset-Backed Securities (cont'd)
GAIA Aviation Ltd.,
7.00%, 12/15/44 (b)	$	1,274	$	591
Goodgreen Trust,
5.53%, 4/15/55 (b)		2,895		2,932
Home Partners of America Trust,
1 Month USD LIBOR + 1.45%, 1.60%, 7/17/37 (b)(c)		2,200		2,181
Invitation Homes Trust,
1 Month USD LIBOR + 2.00%, 2.15%, 6/17/37 (b)(c)		2,500		2,514
1 Month USD LIBOR + 2.25%, 2.50%, 7/17/37 (b)(c)		132		131
JOL Air Ltd.,
4.95%, 4/15/44 (b)		241		175
Lunar Aircraft Ltd.,
3.38%, 2/15/45 (b)		468		438
MACH 1 Cayman Ltd.,
3.47%, 10/15/39 (b)		1,114		1,024
MAPS Ltd.,
4.21%, 5/15/43 (b)		580		539
METAL LLC,
4.58%, 10/15/42 (b)		623		473
MFA LLC,
3.35%, 11/25/47 (b)		613		616
3.88%, 5/25/48 (b)		874		874
4.16%, 7/25/48 (b)		660		662
Mosaic Solar Loan Trust,
2.10%, 4/20/46 (b)		1,045		1,071
Nationstar HECM Loan Trust,
2.82%, 9/25/30 (b)(c)		775		775
Navistar Financial Dealer Note Master Trust,
1 Month USD LIBOR + 2.90%, 3.05%, 7/25/25 (b)(c)		1,300		1,309
New Residential Advance Receivables Trust,
2.80%, 10/15/51 (b)		600		601
New Residential Mortgage LLC,
5.44%, 7/25/25 (b)		2,818		2,829
New Residential Mortgage LLC,
4.69%, 5/25/23 (b)		333		325
NewDay Funding PLC,
1 Month GBP LIBOR + 2.10%, 2.15%, 8/15/26 (b)(c)	GBP	500		637
Newtek Small Business Loan Trust,
1 Month USD LIBOR + 1.70%, 1.85%, 2/25/44 (b)(c)	$	563		550
NRZ Excess Spread-Collateralized Notes,
4.37%, 1/25/23 (b)		332		328
4.59%, 2/25/23 (b)		603		583
5.44%, 6/25/25 (b)		2,671		2,696
NYCTL Trust,
2.19%, 11/10/32 (b)		1,297		1,315

	Face Amount (000)		Value (000)
Oxford Finance Funding LLC,
3.10%, 2/15/28 (b)	$	1,000	$	1,017
5.44%, 2/15/27 (b)		550		556
PNMAC GMSR Issuer Trust,
1 Month USD LIBOR + 2.35%, 2.50%, 4/25/23 (b)(c)		1,050		1,013
1 Month USD LIBOR + 2.65%, 2.80%, 8/25/25 (b)(c)		1,400		1,354
1 Month USD LIBOR + 2.85%, 3.00%, 2/25/23 (b)(c)		500		492
Pretium Mortgage Credit Partners I LLC,
2.86%, 5/27/59 (b)		2,009		2,004
Prosper Marketplace Issuance Trust,
3.20%, 2/17/26 (b)		1,150		1,155
3.59%, 7/15/25 (b)		1,250		1,259
4.87%, 6/17/24 (b)		120		120
5.50%, 10/15/24 (b)		2,000		1,972
PRPM LLC,
3.35%, 11/25/24 (b)		986		990
3.97%, 4/25/24 (b)		924		934
Raptor Aircraft Finance I LLC,
4.21%, 8/23/44 (b)		2,307		2,064
RCO V Mortgage LLC,
3.47%, 11/25/24 (b)		1,979		1,978
4.46%, 10/25/23 (b)		2		2
ReadyCap Lending Small Business Loan Trust,
Daily U.S. Prime Rate – 0.50%, 2.75%, 12/27/44 (b)(c)		828		774
Republic Finance Issuance Trust,
3.43%, 11/22/27 (b)		1,100		1,119
3.93%, 11/22/27 (b)		500		495
S-Jets Ltd.,
7.02%, 8/15/42 (b)		1,008		445
SFS Asset Securitization LLC,
4.24%, 6/10/25 (b)		2,137		2,133
SLM Student Loan Trust,
3 Month EURIBOR + 0.55%, 0.10%, 7/25/39 - 1/25/40 (c)	EUR	3,900		4,208
Small Business Lending Trust,
2.85%, 7/15/26 (b)	$	292		287
Small Business Origination Loan Trust,
3.85%, 12/15/27 (c)	GBP	751		529
Sofi Consumer Loan Program Trust,
3.79%, 4/26/27 (b)	$	600		616
4.02%, 8/25/27 (b)		200		203
Sprite 2017-1 Ltd.,
4.25%, 12/15/37 (b)		517		472
SPS Servicer Advance Receivables Trust Advance Receivables Backed Notes,
2.77%, 10/15/52 (b)		1,000		992
START Ireland,
4.09%, 3/15/44 (b)		363		342
Start Ltd.,
4.09%, 5/15/43 (b)		1,308		1,222

The accompanying notes are an integral part of the financial statements.
7

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Core Plus Fixed Income Portfolio

	Face Amount (000)		Value (000)
Asset-Backed Securities (cont'd)
Tricon American Homes Trust,
5.10%, 1/17/36 (b)	$	1,500	$	1,564
5.15%, 9/17/34 (b)		1,200		1,235
5.77%, 11/17/33 (b)		1,300		1,292
Upgrade Receivables Trust,
5.17%, 11/15/24 (b)		1,500		1,493
Upstart Securitization Trust,
3.73%, 9/20/29 (b)		1,700		1,695
5.00%, 8/20/25 (b)		59		59
Vantage Data Centers Issuer LLC,
4.07%, 2/16/43 (b)		390		404
VCAT LLC,
3.57%, 11/25/49 (b)(c)		1,078		1,077
3.67%, 8/25/50 (b)		2,944		2,949
Vericrest Opportunity Loan Trust,
3.18%, 10/25/49 (b)		979		982
3.35%, 9/25/49 (b)		1,415		1,419
Verizon Owner Trust,
1.94%, 4/22/24		1,700		1,741
VOLT LXXX LLC,
3.23%, 10/25/49 (b)		825		826
VOLT LXXXIII LLC,
3.33%, 11/26/49 (b)		1,597		1,604
VOLT LXXXV LLC,
3.23%, 1/25/50 (b)		1,201		1,205
VOLT LXXXVIII LLC,
2.98%, 3/25/50 (b)		1,834		1,834
				110,282
Collateralized Mortgage Obligations — Agency Collateral Series (0.4%)
Federal Home Loan Mortgage Corporation,
IO
2.83%, 8/25/48 (c)		5,484		1,153
Federal Home Loan Mortgage Corporation,
1 Month USD LIBOR + 4.35%, 4.51%, 12/25/26 (b)(c)		114		113
1 Month USD LIBOR + 5.05%, 5.21%, 7/25/23 (c)		99		96
1 Month USD LIBOR + 5.25%, 5.41%, 7/25/26 (b)(c)		46		47
IO
0.46%, 11/25/27 (c)		23,788		531
0.56%, 8/25/27 (c)		14,735		402
3.57%, 10/25/38 (c)		3,500		1,175
IO REMIC
6.00% - 1 Month USD LIBOR, 5.85%, 11/15/43 (d)		778		134
6.05% - 1 Month USD LIBOR, 5.90%, 4/15/39 (d)		236		4
IO STRIPS
7.50%, 12/15/29		21		4

	Face Amount (000)		Value (000)
Federal National Mortgage Association,
IO PAC REMIC
8.00%, 9/18/27	$	64	$	10
IO REMIC
6.00%, 7/25/33		50		7
IO STRIPS
6.50%, 9/25/29 - 12/25/29		277		39
8.00%, 4/25/24		31		1
8.50%, 10/25/25		21		3
9.00%, 11/25/26		21		2
REMIC
7.00%, 9/25/32		155		188
Government National Mortgage Association,
IO
5.00%, 2/16/41		161		29
IO PAC
6.15% - 1 Month USD LIBOR, 5.99%, 10/20/41 (d)		556		26
				3,964
Commercial Mortgage-Backed Securities (5.1%)
Bancorp Commercial Mortgage Trust,
1 Month USD LIBOR + 2.30%, 2.45%, 9/15/36 (b)(c)		1,400		1,297
BANK 2019-BNK21,
IO
1.00%, 10/17/52 (c)		14,956		970
Barclays Commercial Mortgage Trust,
IO
1.51%, 5/15/52 (c)		17,937		1,679
Benchmark Mortgage Trust,
3.76%, 7/15/53 (b)		2,000		2,017
IO
0.99%, 9/15/48 (b)(c)		31,000		1,482
BF 2019-NYT Mortgage Trust,
1 Month USD LIBOR + 1.70%, 1.85%, 12/15/35 (b)(c)		2,500		2,497
BXP Trust,
1 Month USD LIBOR + 3.00%, 3.15%, 11/15/34 (b)(c)		1,150		874
CG-CCRE Commercial Mortgage Trust,
1 Month USD LIBOR + 1.85%, 2.01%, 11/15/31 (b)(c)		761		712
Citigroup Commercial Mortgage Trust,
3.62%, 12/10/41 (b)		1,100		866
IO
0.98%, 11/10/48 (c)		2,632		76
1.04%, 9/10/58 (c)		4,588		168
COMM Mortgage Trust,
3.51%, 8/15/57 (b)(c)		1,400		1,327
5.46%, 8/10/46 (b)(c)		800		664
IO
0.14%, 7/10/45 (c)		12,527		26
0.88%, 10/10/47 (c)		3,198		73
1.15%, 7/15/47 (c)		3,021		93

The accompanying notes are an integral part of the financial statements.
8

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Core Plus Fixed Income Portfolio

	Face Amount (000)		Value (000)
Commercial Mortgage-Backed Securities (cont'd)
CSWF 2018-TOP,
1 Month USD LIBOR + 1.45%, 1.60%, 8/15/35 (b)(c)	$	2,240	$	2,143
GS Mortgage Securities Trust,
4.90%, 8/10/46 (b)(c)		500		384
IO
0.87%, 9/10/47 (c)		5,124		122
1.40%, 10/10/48 (c)		5,012		245
InTown Hotel Portfolio Trust,
1 Month USD LIBOR + 2.05%, 2.20%, 1/15/33 (b)(c)		579		562
Jackson Park Trust LIC,
3.24%, 10/14/39 (b)(c)		1,700		1,624
JP Morgan Chase Commercial Mortgage Securities Trust,
IO
0.65%, 4/15/46 (c)		6,956		90
0.82%, 12/15/49 (c)		4,136		116
1.09%, 7/15/47 (c)		7,168		132
JPMBB Commercial Mortgage Securities Trust,
4.83%, 4/15/47 (b)(c)		775		684
IO
1.16%, 8/15/47 (c)		3,867		113
Manhattan West,
2.41%, 9/10/39 (b)(c)		1,500		1,468
MFT Trust,
3.39%, 8/10/40 (b)(c)		1,000		932
3.48%, 2/10/42 (b)(c)		800		746
MKT 2020-525M Mortgage Trust,
2.94%, 2/12/40 (b)(c)		1,000		908
Multifamily Connecticut Avenue Securities Trust,
1 Month USD LIBOR + 1.70%, 1.85%, 10/15/49 (b)(c)		473		454
1 Month USD LIBOR + 1.95%, 2.10%, 3/25/50 (b)(c)		2,992		2,917
Natixis Commercial Mortgage Securities Trust,
1 Month USD LIBOR + 2.20%, 2.35%, 7/15/36 (b)(c)		2,300		2,217
4.27%, 5/15/39(b)(c)		2,300		2,337
4.46%, 1/15/43 (b)(c)		800		802
4.56%, 2/15/39 (b)(c)		1,941		1,930
Olympic Tower 2017-OT Mortgage Trust,
3.57%, 5/10/39 (b)		2,900		3,128
SG Commercial Mortgage Securities Trust,
3.85%, 3/15/37 (b)(c)		1,900		1,740
4.66%, 2/15/41 (b)(c)		1,250		1,141
VMC Finance 2019-FL3 LLC,
1 Month USD LIBOR + 2.05%, 2.20%, 9/15/36 (b)(c)		1,603		1,551
Wells Fargo Commercial Mortgage Trust,
1 Month USD LIBOR + 1.74%, 1.89%, 2/15/37 (b)(c)		900		802
1 Month USD LIBOR + 2.21%, 2.36%, 1/15/35 (b)(c)		500		469

	Face Amount (000)		Value (000)
WFRBS Commercial Mortgage Trust,
3.50%, 8/15/47 (b)	$	1,400	$	1,010
4.28%, 5/15/45 (b)(c)		425		398
				45,986
Corporate Bonds (36.0%)
Energy (0.5%)
BP Capital Markets America, Inc.,
3.12%, 5/4/26		2,250		2,486
3.25%, 5/6/22		625		652
Midwest Connector Capital Co. LLC,
3.63%, 4/1/22 (b)(e)		400		403
Petrobras Global Finance BV,
6.75%, 6/3/50		710		770
				4,311
Finance (14.2%)
AerCap Ireland Capital DAC/AerCap Global Aviation Trust,
4.13%, 7/3/23		1,150		1,174
Aflac, Inc.,
3.60%, 4/1/30		1,250		1,470
Air Lease Corp.,
2.30%, 2/1/25		1,325		1,305
American Express Co.,
4.20%, 11/6/25		1,625		1,884
American International Group, Inc.,
4.50%, 7/16/44		1,075		1,258
4.88%, 6/1/22		375		402
Aon Corp.,
2.20%, 11/15/22		1,250		1,294
AvalonBay Communities, Inc., Series G
2.95%, 5/11/26		375		416
Avolon Holdings Funding Ltd.,
2.88%, 2/15/25 (b)		1,750		1,607
Banco Bradesco SA,
3.20%, 1/27/25 (b)		2,790		2,838
Banco Santander Chile,
2.70%, 1/10/25 (b)		1,125		1,188
Banco Santander SA,
5.18%, 11/19/25		600		680
Bank of America Corp.,
2.59%, 4/29/31		1,275		1,360
2.68%, 6/19/41		603		619
3.19%, 7/23/30		475		523
4.24%, 4/24/38		94		115
4.25%, 10/22/26		2,288		2,653
MTN
4.00%, 1/22/25		1,055		1,176
Bank of Montreal,
3.80%, 12/15/32		1,675		1,868
Bank of New York Mellon Corp. (The), MTN
3.65%, 2/4/24		1,750		1,922

The accompanying notes are an integral part of the financial statements.
9

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Core Plus Fixed Income Portfolio

	Face Amount (000)		Value (000)
Finance (cont'd)
Banque Federative du Credit Mutuel SA,
3.75%, 7/20/23 (b)	$	1,530	$	1,661
BBVA USA,
3.50%, 6/11/21		800		815
Belrose Funding Trust,
2.33%, 8/15/30 (b)		2,800		2,773
BNP Paribas SA,
2.82%, 11/19/25 (b)		700		738
4.40%, 8/14/28 (b)		1,050		1,233
Boston Properties LP,
3.80%, 2/1/24		700		759
BPCE SA,
5.15%, 7/21/24 (b)		1,075		1,206
Brookfield Finance LLC,
3.45%, 4/15/50		1,350		1,325
Brookfield Finance, Inc.,
4.00%, 4/1/24		775		854
Brown & Brown, Inc.,
2.38%, 3/15/31		900		908
4.20%, 9/15/24		1,150		1,270
Canadian Imperial Bank of Commerce,
2.25%, 1/28/25		2,300		2,429
Capital One Bank USA NA,
3.38%, 2/15/23		925		979
Capital One Financial Corp.,
3.30%, 10/30/24		3,525		3,824
Chubb INA Holdings, Inc.,
1.38%, 9/15/30		2,275		2,253
Citigroup, Inc.,
2.57%, 6/3/31		425		446
2.67%, 1/29/31		4,375		4,614
2.98%, 11/5/30		932		1,009
5.30%, 5/6/44		50		67
6.68%, 9/13/43		70		108
Citizens Bank NA, MTN
2.55%, 5/13/21		250		253
CNO Financial Group, Inc.,
5.25%, 5/30/29		885		1,025
Cooperatieve Rabobank UA,
3.95%, 11/9/22		650		691
Credit Agricole SA,
3.75%, 4/24/23 (b)		1,175		1,260
Credit Suisse Group AG,
2.59%, 9/11/25 (b)		2,125		2,220
Crown Castle International Corp.,
3.30%, 7/1/30		950		1,041
4.15%, 7/1/50		725		832
CyrusOne LP/CyrusOne Finance Corp.,
2.90%, 11/15/24		200		212
Danske Bank A/S,
5.00%, 1/12/23 (b)		350		367

	Face Amount (000)		Value (000)
Deutsche Bank AG,
3.95%, 2/27/23	$	850	$	892
GE Capital International Funding Co. Unlimited Co.,
4.42%, 11/15/35		1,315		1,391
GLP Capital LP/GLP Financing II, Inc.,
3.35%, 9/1/24		1,900		1,934
Goldman Sachs Group, Inc. (The),
3.69%, 6/5/28		775		870
6.75%, 10/1/37		965		1,405
MTN
4.80%, 7/8/44		625		821
Grupo Aval Ltd.,
4.38%, 2/4/30 (b)		770		745
Harborwalk Funding Trust,
5.08%, 2/15/69 (b)		950		1,177
HSBC Holdings PLC,
4.25%, 3/14/24		2,325		2,494
HSBC USA, Inc.,
3.50%, 6/23/24		1,450		1,567
ING Bank N.V.,
5.80%, 9/25/23 (b)		204		229
Intercontinental Exchange, Inc.,
1.85%, 9/15/32		2,675		2,673
Intesa Sanpaolo SpA,
5.25%, 1/12/24		610		676
Itau Unibanco Holding SA,
2.90%, 1/24/23 (b)		3,100		3,140
Jefferies Finance LLC/JFIN Co-Issuer Corp.,
6.25%, 6/3/26 (b)		1,325		1,351
JPMorgan Chase & Co.,
3.70%, 5/6/30		3,750		4,310
4.13%, 12/15/26		1,600		1,862
Kimco Realty Corp.,
3.70%, 10/1/49		1,050		1,034
Lloyds Banking Group PLC,
3.57%, 11/7/28		250		274
4.38%, 3/22/28		1,525		1,770
Macquarie Bank Ltd.,
2.30%, 1/22/25 (b)(e)		1,700		1,802
Marsh & McLennan Cos., Inc.,
2.25%, 11/15/30		2,025		2,123
MassMutual Global Funding II,
3.40%, 3/8/26 (b)		1,040		1,175
MetLife, Inc.,
5.88%, 2/6/41		150		219
Metropolitan Life Global Funding I,
2.95%, 4/9/30 (b)		1,300		1,461
Mizuho Financial Group, Inc.,
2.63%, 4/12/21 (b)		600		607
MPT Operating Partnership LP/MPT Finance Corp.,
5.00%, 10/15/27		965		1,008

The accompanying notes are an integral part of the financial statements.
10

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Core Plus Fixed Income Portfolio

	Face Amount (000)		Value (000)
Finance (cont'd)
Nationwide Building Society,
3.96%, 7/18/30 (b)	$	350	$	396
4.30%, 3/8/29 (b)		1,550		1,753
4.36%, 8/1/24 (b)		500		543
New York Life Global Funding,
1.70%, 9/14/21 (b)		600		609
Oversea-Chinese Banking Corp. Ltd.,
1.83%, 9/10/30 (b)(e)		970		969
Pine Street Trust I,
4.57%, 2/15/29 (b)		575		669
PNC Financial Services Group, Inc. (The),
2.20%, 11/1/24		1,650		1,747
Progressive Corp. (The),
3.20%, 3/26/30		725		831
4.00%, 3/1/29		575		694
Quicken Loans LLC/Quicken Loans Co-Issuer, Inc.,
3.88%, 3/1/31 (b)		1,350		1,337
Realty Income Corp.,
3.25%, 10/15/22		400		420
Royal Bank of Scotland Group PLC,
3.88%, 9/12/23		875		939
Santander UK Group Holdings PLC,
3.57%, 1/10/23		2,400		2,481
Skandinaviska Enskilda Banken AB,
2.63%, 11/17/20 (b)		500		502
Societe Generale SA,
2.63%, 1/22/25 (b)		1,625		1,678
Standard Chartered PLC,
3.05%, 1/15/21 (b)		325		327
4.64%, 4/1/31 (b)		526		607
Syngenta Finance N.V.,
4.89%, 4/24/25 (b)		975		1,058
TD Ameritrade Holding Corp.,
3.63%, 4/1/25		500		561
Travelers Cos., Inc. (The),
3.75%, 5/15/46		800		941
UnitedHealth Group, Inc.,
2.88%, 3/15/23		1,025		1,086
3.75%, 7/15/25		1,675		1,914
University of Chicago (The), Series C
2.55%, 4/1/50		620		622
WEA Finance LLC/Westfield UK & Europe Finance PLC,
3.25%, 10/5/20 (b)		314		314
Wells Fargo & Co.,
2.57%, 2/11/31		500		526
2.88%, 10/30/30		675		726
5.01%, 4/4/51		1,000		1,376
				127,560

	Face Amount (000)		Value (000)
Industrials (19.2%)
AbbVie, Inc.,
3.20%, 11/21/29 (b)	$	4,825	$	5,337
Adobe, Inc.,
2.30%, 2/1/30		1,975		2,129
Air Liquide Finance SA,
1.75%, 9/27/21 (b)		450		456
Airbus SE,
0.00%, 6/14/21	EUR	800		933
Akamai Technologies, Inc.,
0.38%, 9/1/27	$	371		431
Albertsons Cos., Inc./Safeway, Inc./ New Albertsons LP/Albertsons LLC,
3.50%, 2/15/23 (b)		700		712
Amazon.com, Inc.,
2.50%, 6/3/50		775		795
2.80%, 8/22/24		1,625		1,760
4.25%, 8/22/57		375		514
American Airlines Pass-Through Trust, Series AA
3.15%, 8/15/33		531		503
Amgen, Inc.,
2.45%, 2/21/30		1,925		2,045
2.77%, 9/1/53 (b)		600		578
4.66%, 6/15/51		75		98
Anheuser-Busch InBev Worldwide, Inc.,
4.60%, 4/15/48		725		867
4.75%, 1/23/29		725		886
5.55%, 1/23/49		1,125		1,517
Anthem, Inc.,
2.38%, 1/15/25		550		585
3.65%, 12/1/27		1,650		1,882
Apple, Inc.,
2.95%, 9/11/49		2,025		2,225
3.20%, 5/13/25		450		502
AT&T, Inc.,
2.25%, 2/1/32		1,950		1,957
3.50%, 9/15/53 (b)		652		633
3.65%, 9/15/59 (b)		1,375		1,358
Automatic Data Processing, Inc.,
1.25%, 9/1/30		2,250		2,225
BAT Capital Corp.,
3.56%, 8/15/27		2,100		2,271
Becton Dickinson and Co.,
2.89%, 6/6/22		600		621
Berry Global, Inc.,
4.50%, 2/15/26 (b)(e)		1,635		1,654
Boeing Co. (The),
3.95%, 8/1/59		850		771
5.15%, 5/1/30		1,700		1,916
Booking Holdings, Inc.,
0.90%, 9/15/21		275		293

The accompanying notes are an integral part of the financial statements.
11

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Core Plus Fixed Income Portfolio

	Face Amount (000)		Value (000)
Industrials (cont'd)
BP Capital Markets PLC,
4.38%, 6/22/25 (f)	$	700	$	731
4.88%, 3/22/30 (f)		700		751
Braskem Netherlands Finance BV,
4.50%, 1/31/30 (b)		1,200		1,122
Campbell Soup Co.,
3.13%, 4/24/50		1,375		1,398
Canadian National Railway Co.,
2.45%, 5/1/50		900		898
Charter Communications Operating LLC/ Charter Communications Operating Capital,
2.80%, 4/1/31		1,250		1,304
Children's Health System of Texas,
2.51%, 8/15/50		800		762
Cigna Corp.,
2.40%, 3/15/30		2,150		2,234
3.05%, 10/15/27		350		390
CNH Industrial Capital LLC,
4.38%, 11/6/20 (e)		625		627
CNOOC Finance 2013 Ltd.,
3.00%, 5/9/23		540		567
Coca-Cola Femsa SAB de CV,
2.75%, 1/22/30		1,600		1,706
Comcast Corp.,
1.95%, 1/15/31		2,350		2,422
2.80%, 1/15/51		825		840
4.05%, 11/1/52		450		555
4.25%, 1/15/33		1,050		1,308
Concho Resources, Inc.,
4.85%, 8/15/48		575		634
Cummins, Inc.,
1.50%, 9/1/30		2,175		2,166
CVS Health Corp.,
1.75%, 8/21/30		425		416
3.75%, 4/1/30		1,182		1,352
5.05%, 3/25/48		1,275		1,633
5.13%, 7/20/45		425		539
Deere & Co.,
3.10%, 4/15/30		500		572
Dell International LLC/EMC Corp.,
6.02%, 6/15/26 (b)		1,475		1,734
Delta Air Lines, Inc., Series AA
3.20%, 10/25/25		1,050		1,049
Diageo Capital PLC,
2.13%, 10/24/24		1,475		1,566
Diamond Sports Group LLC/Diamond Sports Finance Co.,
6.63%, 8/15/27 (b)		700		365
Diamondback Energy, Inc.,
3.25%, 12/1/26		1,750		1,758

	Face Amount (000)		Value (000)
Duke University, Series 2020
2.83%, 10/1/55	$	1,600	$	1,700
Enbridge, Inc.,
2.50%, 1/15/25		925		974
Energy Transfer Operating LP,
2.90%, 5/15/25		1,575		1,586
Enterprise Products Operating LLC,
4.20%, 1/31/50		1,775		1,894
Equinix, Inc.,
1.55%, 3/15/28 (g)		1,675		1,681
Exxon Mobil Corp.,
3.10%, 8/16/49		1,225		1,257
Fiserv, Inc.,
2.65%, 6/1/30		500		539
Ford Motor Credit Co., LLC,
3.10%, 5/4/23		400		392
4.39%, 1/8/26		800		792
Fortune Brands Home & Security, Inc.,
4.00%, 9/21/23		675		739
Fox Corp.,
5.58%, 1/25/49		925		1,282
General Motors Co.,
6.60%, 4/1/36		200		244
General Motors Financial Co., Inc.,
3.85%, 1/5/28		800		842
4.35%, 1/17/27		1,825		1,985
Georgia-Pacific LLC,
2.30%, 4/30/30 (b)		1,525		1,622
Glencore Funding LLC,
4.13%, 3/12/24 (b)		2,375		2,576
Grifols SA,
2.25%, 11/15/27 (b)	EUR	800		934
HCA, Inc.,
5.50%, 6/15/47	$	1,100		1,367
Heathrow Funding Ltd.,
4.88%, 7/15/23 (b)		525		538
Imperial Brands Finance PLC,
3.13%, 7/26/24 (b)		1,000		1,059
Intel Corp.,
3.25%, 11/15/49		1,500		1,686
International Business Machines Corp.,
3.30%, 5/15/26		2,750		3,099
J2 Global, Inc.,
1.75%, 11/1/26 (b)		825		734
Jazz Investments I Ltd.,
1.88%, 8/15/21		1,000		1,015
Johns Hopkins University, Series A
2.81%, 1/1/60		1,170		1,248
Kimberly-Clark de Mexico SAB de CV,
2.43%, 7/1/31 (b)		1,375		1,402

The accompanying notes are an integral part of the financial statements.
12

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Core Plus Fixed Income Portfolio

	Face Amount (000)		Value (000)
Industrials (cont'd)
Las Vegas Sands Corp.,
3.20%, 8/8/24	$	850	$	860
Level 3 Financing, Inc.,
3.40%, 3/1/27 (b)		1,275		1,376
Lowe's Cos., Inc.,
2.50%, 4/15/26		775		841
4.50%, 4/15/30		475		591
LYB International Finance III LLC,
4.20%, 5/1/50		550		616
Marriott Vacations Worldwide Corp.,
1.50%, 9/15/22		600		593
McLaren Health Care Corp., Series A
4.39%, 5/15/48		1,175		1,469
Methodist Hospital (The), Series 20A
2.71%, 12/1/50		1,520		1,526
Microsoft Corp.,
2.53%, 6/1/50		750		789
3.13%, 11/3/25		325		364
Mondelez International Holdings Netherlands BV,
2.25%, 9/19/24 (b)		2,925		3,081
Newcastle Coal Infrastructure Group Pty Ltd.,
4.40%, 9/29/27 (b)		1,375		1,371
Newmont Corp.,
2.25%, 10/1/30		1,150		1,190
3.70%, 3/15/23 (e)		39		41
NIKE, Inc.,
2.85%, 3/27/30		1,225		1,379
Nissan Motor Co. Ltd.,
3.04%, 9/15/23 (b)		1,325		1,344
Nuance Communications, Inc.,
1.00%, 12/15/35		425		619
Nvent Finance Sarl,
3.95%, 4/15/23		775		809
NVIDIA Corp.,
2.85%, 4/1/30		1,250		1,408
Occidental Petroleum Corp.,
3.20%, 8/15/26		160		127
5.55%, 3/15/26		925		839
Oracle Corp.,
2.50%, 4/1/25		1,900		2,039
4.00%, 7/15/46		1,050		1,249
Palo Alto Networks, Inc.,
0.75%, 7/1/23		515		582
Procter & Gamble Co. (The),
3.00%, 3/25/30		1,050		1,220
Pure Storage, Inc.,
0.13%, 4/15/23		170		165
Raytheon Technologies Corp.,
4.50%, 6/1/42		475		601

	Face Amount (000)		Value (000)
Resorts World Las Vegas LLC/RWLV Capital, Inc.,
4.63%, 4/16/29 (b)	$	2,000	$	1,889
Rockies Express Pipeline LLC,
3.60%, 5/15/25 (b)		2,125		2,088
Royalty Pharma PLC,
2.20%, 9/2/30 (b)		2,000		2,001
Shell International Finance BV,
3.25%, 5/11/25		1,150		1,273
Sherwin-Williams Co. (The),
2.30%, 5/15/30		1,850		1,937
2.95%, 8/15/29		625		689
Siemens Financieringsmaatschappij N.V.,
2.35%, 10/15/26 (b)		2,050		2,203
Sprint Spectrum Co., LLC/Sprint Spectrum Co., II LLC/Sprint Spectrum Co., III LLC,
3.36%, 3/20/23 (b)		847		858
Standard Industries, Inc.,
2.25%, 11/21/26 (b)	EUR	575		647
Starbucks Corp.,
3.80%, 8/15/25	$	1,550		1,754
Sunoco Logistics Partners Operations LP,
3.90%, 7/15/26		750		771
T-Mobile USA, Inc.,
3.88%, 4/15/30 (b)		1,700		1,931
Target Corp.,
2.65%, 9/15/30		500		560
Telefonica Emisiones SA,
4.10%, 3/8/27		1,800		2,050
Teva Pharmaceutical Finance Netherlands III BV,
2.20%, 7/21/21		162		161
TJX Cos., Inc. (The),
3.88%, 4/15/30		1,625		1,930
Total Capital International SA,
2.88%, 2/17/22		500		517
Trimble, Inc.,
4.15%, 6/15/23		1,150		1,240
TSMC Global Ltd.,
0.75%, 9/28/25 (b)(e)		1,325		1,314
Twitter, Inc.,
0.25%, 6/15/24		1,000		1,118
1.00%, 9/15/21		1,433		1,428
Upjohn, Inc.,
4.00%, 6/22/50 (b)		725		778
Verint Systems, Inc.,
1.50%, 6/1/21		325		330
Verizon Communications, Inc.,
3.88%, 2/8/29		375		445
4.67%, 3/15/55		1,671		2,324
Visa, Inc.,
1.10%, 2/15/31		1,500		1,477
Volkswagen Group of America Finance LLC,
4.75%, 11/13/28 (b)		1,025		1,227

The accompanying notes are an integral part of the financial statements.
13

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Core Plus Fixed Income Portfolio

	Face Amount (000)		Value (000)
Industrials (cont'd)
VTR Finance,
6.38%, 7/15/28 (b)	$	1,050	$	1,108
Walmart, Inc.,
3.70%, 6/26/28		250		296
4.05%, 6/29/48		200		262
Walt Disney Co. (The),
2.75%, 9/1/49		1,766		1,729
3.60%, 1/13/51		281		318
Weibo Corp.,
1.25%, 11/15/22		332		317
Western Midstream Operating LP,
4.10%, 2/1/25		1,200		1,145
Williams Cos., Inc. (The),
4.85%, 3/1/48		1,325		1,487
Zillow Group, Inc.,
2.00%, 12/1/21		637		1,237
				172,968
Utilities (2.1%)
Boston Gas Co.,
3.00%, 8/1/29 (b)		1,150		1,267
Calpine Corp.,
4.50%, 2/15/28 (b)		1,450		1,487
DTE Energy Co.,
2.95%, 3/1/30		800		859
Duke Energy Indiana LLC, Series YYY
3.25%, 10/1/49		450		503
Enel Finance International N.V.,
3.63%, 5/25/27 (b)		350		390
4.25%, 9/14/23 (b)		575		630
Entergy Louisiana LLC,
3.05%, 6/1/31		525		601
FirstEnergy Corp., Series C
3.40%, 3/1/50		1,300		1,269
Korea Hydro & Nuclear Power Co., Ltd.,
3.75%, 7/25/23 (b)		1,380		1,497
Mississippi Power Co.,
3.95%, 3/30/28		2,325		2,672
Northern States Power Co.,
2.90%, 3/1/50		825		887
Oglethorpe Power Corp.,
5.05%, 10/1/48		1,325		1,572
ONEOK, Inc.,
3.10%, 3/15/30		1,750		1,688
Pacific Gas and Electric Co.,
3.15%, 1/1/26 (e)		1,000		1,028
3.50%, 8/1/50		1,275		1,157
Xcel Energy, Inc.,
2.60%, 12/1/29		1,375		1,488
				18,995
				323,834

	Face Amount (000)		Value (000)
Mortgages — Other (9.5%)
Adjustable Rate Mortgage Trust,
3.90%, 6/25/35 (c)	$	170	$	168
Alternative Loan Trust,
1 Month USD LIBOR + 0.18%, 0.33%, 5/25/47 (c)		115		106
Banc of America Alternative Loan Trust,
1 Month USD LIBOR + 0.65%, 0.80%, 7/25/46 (c)		158		116
5.86%, 10/25/36		484		218
6.00%, 4/25/36		5		5
Banc of America Funding Trust,
5.25%, 7/25/37		78		77
Bear Stearns ARM Trust,
3.85%, 2/25/34 (c)		714		707
Bunker Hill Loan Depositary Trust,
1.72%, 2/25/55 (b)(c)		2,850		2,884
Cascade Funding Mortgage Trust,
4.00%, 10/25/68 (b)(c)		1,832		1,793
CFMT 2020-ABC1 LLC,
1.94%, 9/25/50 (b)(c)		4,325		4,325
ChaseFlex Trust,
6.00%, 2/25/37		672		424
Classic RMBS Trust,
3.06%, 8/16/49 (b)	CAD	2,068		1,561
E-MAC NL BV,
3 Month EURIBOR + 0.18%, 1.81%, 7/25/36 (c)	EUR	490		555
Eurosail BV,
3 Month EURIBOR + 1.80%, 1.36%, 10/17/40 (c)		700		803
Eurosail PLC,
3 Month GBP LIBOR + 0.95%, 1.01%, 6/13/45 (c)	GBP	674		851
Farringdon Mortgages No. 2 PLC,
3 Month GBP LIBOR + 1.50%, 1.58%, 7/15/47 (c)		209		267
Federal Home Loan Mortgage Corporation,
3.00%, 7/25/46 - 5/25/47	$	3,214		3,279
3.50%, 5/25/45 - 5/25/47		1,430		1,484
3.88%, 5/25/45 (b)(c)		42		42
4.00%, 5/25/45		53		56
1 Month USD LIBOR + 2.35%, 2.50%, 4/25/30 (c)		956		966
1 Month USD LIBOR + 5.15%, 5.30%, 10/25/29 (c)		300		307
FMC GMSR Issuer Trust,
4.23%, 9/25/24 (b)(c)		1,900		1,864
5.07%, 5/25/24 (b)(c)		1,400		1,418
GCAT Trust,
2.65%, 10/25/68 (b)(c)		967		1,010
Grifonas Finance PLC,
6 Month EURIBOR + 0.28%, 0.00%, 8/28/39 (c)	EUR	359		407

The accompanying notes are an integral part of the financial statements.
14

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Core Plus Fixed Income Portfolio

	Face Amount (000)		Value (000)
Mortgages — Other (cont'd)
HarborView Mortgage Loan Trust,
1 Month USD LIBOR + 0.19%, 0.35%, 1/19/38 (c)	$	417	$	379
Headlands Residential LLC,
3.97%, 6/25/24 (b)		500		504
IM Pastor 3 FTH,
3 Month EURIBOR + 0.14%, 0.00%, 3/22/43 (c)	EUR	521		548
JP Morgan Mortgage Trust,
3.79%, 6/25/37 (c)	$	101		89
6.00%, 6/25/37		55		59
L1C 2020-1 LLC,
5.29%, 8/25/51 (b)		1,600		1,604
Landmark Mortgage Securities No. 1 PLC,
3 Month EURIBOR + 0.60%, 0.25%, 6/17/38 (c)	EUR	768		838
Lehman Mortgage Trust,
6.50%, 9/25/37	$	701		366
LHOME Mortgage Trust,
3.23%, 10/25/24 (b)		675		677
4.58%, 10/25/23 (b)		1,000		1,018
New Residential Mortgage Loan Trust,
3.23%, 8/25/60 (b)		557		558
New Residential Mortgage Loan Trust,
4.00%, 9/25/57 (b)(c)		787		870
Newgate Funding PLC,
3 Month GBP LIBOR + 0.16%, 0.22%, 12/15/50 (c)	GBP	1,400		1,699
NRPL Trust,
4.25%, 7/25/67 (b)	$	950		980
OBX 2020-EXP1 Trust,
3.50%, 2/25/60 (b)(c)		1,018		1,053
OBX Trust,
3.50%, 10/25/59 (b)(c)		809		834
Paragon Mortgages No. 13 PLC,
3 Month GBP LIBOR + 0.40%, 0.48%, 1/15/39 (c)	GBP	268		330
Paragon Mortgages No. 15 PLC,
3 Month EURIBOR + 0.54%, 0.06%, 12/15/39 (c)	EUR	800		850
Pepper Residential Securities Trust,
1 Month USD LIBOR + 0.93%, 1.08%, 3/12/61 (b)(c)	$	1,536		1,531
Preston Ridge Partners LLC,
1.00%, 9/25/25		3,000		3,000
PRPM LLC,
3.50%, 10/25/24 (b)(c)		1,733		1,738
4.50%, 1/25/24 (b)		829		837
RMF Buyout Issuance Trust,
1.71%, 6/25/30 (b)(c)		1,987		1,993
2.15%, 6/25/30 (b)(c)		750		753
Rochester Financing No. 2 PLC,
3 Month GBP LIBOR + 2.75%, 2.80%, 6/18/45 (c)	GBP	750		966

	Face Amount (000)		Value (000)
Seasoned Credit Risk Transfer Trust,
3.00%, 9/25/55 - 2/25/59	$	13,394	$	14,599
4.00%, 7/25/56 (c)		450		453
4.00%, 8/25/56 (b)(c)		1,000		982
4.00%, 8/25/58 - 2/25/59		2,106		2,338
4.25%, 8/25/59 (b)(c)		2,700		2,626
4.50%, 6/25/57		2,196		2,464
4.75%, 7/25/56 - 6/25/57(b)(c)		1,408		1,397
4.75%, 10/25/58 (c)		1,300		1,259
Structured Asset Securities Corp. Reverse Mortgage Loan Trust,
1 Month USD LIBOR + 1.85%, 2.00%, 5/25/47 (b)(c)		1,466		1,231
TDA 27 FTA,
3 Month EURIBOR + 0.19%, 0.00%, 12/28/50 (c)	EUR	1,600		1,504
Toorak Mortgage Corp. Ltd.,
3.72%, 9/25/22	$	2,000		2,044
TVC Mortgage Trust,
3.47%, 9/25/24 (b)		850		868
Verus Securitization Trust,
3.72%, 1/25/47 (b)(c)		265		267
Vista Point Securitization Trust,
1.76%, 3/25/65 (b)(c)		3,713		3,742
				85,541
Municipal Bonds (1.2%)
Chicago O'Hare International Airport, IL, O'Hare International Airport Revenue Series 2010B
6.40%, 1/1/40		255		381
City of New York, NY, Series G-1
5.97%, 3/1/36		270		391
Illinois State Toll Highway Authority, IL, Highway Revenue, Build America Bonds Series A
6.18%, 1/1/34		477		692
New York City Transitional Finance Authority Future Tax Secured Revenue, NY, Transitional Finance Authority Future Tax Secured Revenue Series A
5.27%, 5/1/27		320		393
Onondaga Civic Development Corp., NY,
3.07%, 12/1/55		2,925		3,028
Pennsylvania State University/The, PA, Series D
2.84%, 9/1/50		1,425		1,467
University of Virginia, VA,
2.26%, 9/1/50		1,550		1,519
Series C-1
2.97%, 9/1/49		1,440		1,627
Series C-2
2.97%, 9/1/49		1,020		1,157
				10,655

The accompanying notes are an integral part of the financial statements.
15

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Core Plus Fixed Income Portfolio

	Face Amount (000)		Value (000)
Sovereign (7.4%)
Australia Government Bond,
2.75%, 11/21/28	AUD	15,150	$	12,638
3.25%, 4/21/25		10,500		8,529
Banque Ouest Africaine de Developpement,
4.70%, 10/22/31 (b)	$	1,240		1,304
Croatia Government International Bond,
1.50%, 6/17/31	EUR	1,307		1,595
Dominican Republic International Bond,
5.88%, 1/30/60 (b)	$	2,310		2,195
Ecuador Government International Bond,
0.00%, 7/31/30 (b)		62		29
0.50%, 7/31/30 - 7/31/40(b)(h)		1,048		597
Egypt Government International Bond,
6.38%, 4/11/31 (b)	EUR	2,025		2,216
8.15%, 11/20/59 (b)	$	470		440
8.88%, 5/29/50 (b)		410		407
Export-Import Bank of India,
3.25%, 1/15/30 (b)		670		678
3.88%, 2/1/28 (b)		505		532
Honduras Government International Bond,
5.63%, 6/24/30 (b)		350		376
Indonesia Treasury Bond,
8.25%, 5/15/29	IDR	33,797,000		2,481
8.38%, 3/15/34		19,717,000		1,427
Italy Buoni Poliennali Del Tesoro,
1.65%, 12/1/30 (b)	EUR	2,150		2,713
Mexican Bonos, Series M
8.50%, 5/31/29	MXN	70,000		3,746
Mexico Government International Bond,
3.25%, 4/16/30 (e)	$	750		770
New Zealand Government Bond,
2.75%, 4/15/37	NZD	3,925		3,333
Nigeria Government International Bond,
9.25%, 1/21/49 (b)(e)	$	1,620		1,614
Pertamina Persero PT,
6.50%, 11/7/48 (b)		1,325		1,769
Petroleos Mexicanos,
6.50%, 1/23/29		525		472
6.84%, 1/23/30 (b)		570		509
6.95%, 1/28/60 (b)		350		271
7.69%, 1/23/50 (b)		536		449
Qatar Government International Bond,
5.10%, 4/23/48 (b)		1,480		2,061
Republic of Austria Government Bond,
0.85%, 12/31/99 (b)	EUR	290		421
2.10%, 12/31/99 (b)		197		493
Republic of Belarus Ministry of Finance,
6.38%, 2/24/31 (b)	$	1,150		1,079
Republic of South Africa Government Bond,
8.00%, 1/31/30	ZAR	67,793		3,699

	Face Amount (000)		Value (000)
Russian Foreign Bond — Eurobond,
5.63%, 4/4/42	$	1,800	$	2,411
Senegal Government International Bond,
6.25%, 5/23/33 (b)		705		698
Spain Government Bond,
1.25%, 10/31/30 (b)	EUR	3,525		4,545
				66,497
U.S. Treasury Security (1.2%)
U.S. Treasury Bond, 2.25%, 8/15/46	$	9,000		10,656
Variable Rate Senior Loan Interests (1.8%)
American Airlines, Inc.,
2018 Term Loan B
1 Month USD LIBOR + 1.75%,   1.89%, 6/27/25 (c)		990		614
BWAY Holding Co.,
2017 Term Loan B
3 Month USD LIBOR + 3.25%,   3.52%, 4/3/24 (c)		990		933
Carrols Restaurant Group, Inc.,
Term Loan B
3 Month USD LIBOR + 3.25%, 3.40%, 4/30/26 (c)		990		945
Chemours Company (The),
2018 USD Term Loan B
1 Month USD LIBOR + 1.75%, 1.89%, 4/3/25 (c)		992		961
Core & Main LP,
2017 Term Loan B
3 Month USD LIBOR + 2.75%, 3.75%, 8/1/24 (c)		992		978
CPG International, Inc.,
2017 Term Loan
3 Month USD LIBOR + 3.75%, 4.75%, 5/5/24 (c)		218		218
DaVita, Inc.,
2020 Term Loan B
1 Month USD LIBOR + 1.75%, 1.90%, 8/12/26 (c)		993		977
Grifols Worldwide Operations USA, Inc.,
USD 2019 Term Loan B
1 Week USD LIBOR + 2.00%, 2.10%, 11/15/27 (c)		993		974
Hargray Communications Group, Inc.,
2017 Term Loan B
1 Month USD LIBOR + 3.00%, 4.00%, 5/16/24 (c)		992		988
Level 3 Financing Inc.,
2019 Term Loan B
1 Month USD LIBOR + 1.75%, 1.90%, 3/1/27 (c)		1,000		971
Lions Gate Capital Holdings LLC,
2018 Term Loan B
1 Month USD LIBOR + 2.25%, 2.40%, 3/24/25 (c)		990		958

The accompanying notes are an integral part of the financial statements.
16

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Core Plus Fixed Income Portfolio

	Face Amount (000)		Value (000)
Variable Rate Senior Loan Interests (cont'd)
Medallion Midland Acquisition LLC,
1st Lien Term Loan
1 Month USD LIBOR + 3.25%, 4.25%, 10/30/24 (c)	$	794	$	752
Surf Holdings LLC,
USD Term Loan
3 Month USD LIBOR + 3.50%, 3.75%, 3/5/27 (c)		748		734
Surgery Center Holdings, Inc.,
2017 Term Loan B
1 Month USD LIBOR + 3.25%,   4.25%, 9/3/24 (c)		992		938
Univision Communications Inc.,
2020 Replacement Term Loan
1 Month USD LIBOR + 3.75%, 4.75%, 3/13/26 (c)		919		897
Verifone Systems, Inc.,
2018 1st Lien Term Loan
3 Month USD LIBOR + 4.00%, 4.25%, 8/20/25 (c)		992		892
Virgin Media Bristol LLC,
USD Term Loan N
1 Month USD LIBOR + 2.50%, 2.65%, 1/31/28 (c)		1,000		973
Ziggo Financing Partnership,
USD Term Loan I
1 Month USD LIBOR + 2.50%, 2.65%, 4/30/28 (c)		1,500		1,447
				16,150
Total Fixed Income Securities (Cost $861,411)				881,011
	Shares
Short-Term Investments (18.4%)
Securities held as Collateral on Loaned Securities (0.6%)
Investment Company (0.6%)
Morgan Stanley Institutional Liquidity Funds — Government Portfolio — Institutional Class (See Note G) (Cost $5,536)		5,535,980		5,536
Investment Company (17.2%)
Morgan Stanley Institutional Liquidity Funds — Government Portfolio — Institutional Class (See Note G) (Cost $154,471)		154,470,695		154,471
	Face Amount (000)
U.S. Treasury Security (0.3%)
U.S. Treasury Bill
0.16%, 1/28/21 (i)(j) (Cost $2,517)	$	2,518		2,517

	Face Amount (000)		Value (000)
Sovereign (0.3%)
Egypt Treasury Bills,
13.60%, 3/2/21	EGP	3,600	$	218
13.65%, 3/2/21		5,975		361
13.66%, 3/2/21		8,950		541
13.68%, 3/2/21		12,850		777
13.69%, 3/2/21		5,975		361
13.70%, 3/2/21		900		55
Total Sovereign (Cost $2,281)				2,313
Total Short-Term Investments (Cost $164,805)				164,837
Total Investments (116.2%) (Cost $1,026,216) Including $6,455 of Securities Loaned (k)(l)				1,045,848
Liabilities in Excess of Other Assets (–16.2%)				(145,685	)
Net Assets (100.0%)			$	900,163

(a)  Security is subject to delayed delivery.

(b)  144A security — Certain conditions for public sale may exist. Unless otherwise noted, these securities are deemed to be liquid.

(c)  Floating or variable rate securities: The rates disclosed are as of September 30, 2020. For securities based on a published reference rate and spread, the reference rate and spread are indicated in the description in the Portfolio of Investments. Certain variable rate securities may not be based on a published reference rate and spread but are determined by the issuer or agent and are based on current market conditions. These securities do not indicate a reference rate and spread in their description in the Portfolio of Investments.

(d)  Inverse Floating Rate Security — Interest rate fluctuates with an inverse relationship to an associated interest rate. Indicated rate is the effective rate at September 30, 2020.

(e)  All or a portion of this security was on loan at September 30, 2020.

(f)  Perpetual — One or more securities do not have a predetermined maturity date. Rates for these securities are fixed for a period of time, after which they revert to a floating rate. Interest rates in effect are as of September 30, 2020.

(g)  When-issued security.

(h)  Multi-step — Coupon rate changes in predetermined increments to maturity. Rate disclosed is as of September 30, 2020. Maturity date disclosed is the ultimate maturity date.

(i)  All or a portion of the security was pledged to cover margin requirements for swap agreements.

(j)  Rate shown is the yield to maturity at September 30, 2020.

(k)  Securities are available for collateral in connection with purchase of when issued security, securities purchased on a forward commitment basis, open foreign currency forward exchange contracts, futures contracts and swap agreements.

(l)  At September 30, 2020, the aggregate cost for federal income tax purposes is approximately $1,026,013,000. The aggregate gross unrealized appreciation is approximately $32,341,000 and the aggregate gross unrealized depreciation is approximately $13,142,000, resulting in net unrealized appreciation of approximately $19,199,000.

EURIBOR  Euro Interbank Offered Rate.

IO  Interest Only.

LIBOR  London Interbank Offered Rate.

MTN  Medium Term Note.

OAT  Obligations Assimilables du Trésor (French Treasury Obligation).

PAC  Planned Amortization Class.

REMIC  Real Estate Mortgage Investment Conduit.

The accompanying notes are an integral part of the financial statements.
17

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Core Plus Fixed Income Portfolio

STRIPS  Separate Trading of Registered Interest and Principal of Securities.

TBA  To Be Announced.

USD  United States Dollar.

Foreign Currency Forward Exchange Contracts:

The Fund had the following foreign currency forward exchange contracts open at September 30, 2020:

Counterparty	Contracts to Deliver (000)		In Exchange For (000)		Delivery Date	Unrealized Appreciation (Depreciation) (000)
Australia And New Zealand Banking Group	GBP	3,844	$	5,082	12/1/20	$	121
Bank of America NA	ZAR	62,674	$	3,672	12/1/20		(43	)
Barclays Bank PLC	NOK	20,771	$	2,298	12/1/20		71
Barclays Bank PLC	NZD	4,865	$	3,179	12/1/20		(39	)
BNP Paribas SA	EUR	1,868	PLN	8,270	12/1/20		(53	)
BNP Paribas SA	$	2,168	MXN	46,126	12/1/20		(96	)
Citibank NA	EUR	18,614	$	22,183	12/1/20		332
Citibank NA	MXN	35,106	$	1,578	12/1/20		2
Citibank NA	$	3,865	RUB	292,585	12/1/20		(124	)
Goldman Sachs International	RUB	292,585	$	3,906	12/1/20		164
JPMorgan Chase Bank NA	CAD	5,739	$	4,352	12/1/20		40
JPMorgan Chase Bank NA	$	67	CAD	87	12/1/20		(1	)
JPMorgan Chase Bank NA	$	36	GBP	28	12/1/20		—	@
UBS AG	CAD	78	$	59	10/5/20		—	@
UBS AG	AUD	29,604	$	21,246	12/1/20		39
UBS AG	IDR	60,587,262	$	4,086	12/1/20		37
UBS AG	$	59	CAD	78	12/1/20		(—	@)
UBS AG	$	2,184	EUR	1,830	12/1/20		(36	)
UBS AG	$	4,697	NOK	41,220	12/1/20		(277	)
						$	137

Futures Contracts:

The Fund had the following futures contracts open at September 30, 2020:

	Number of Contracts		Expiration Date	Notional Amount (000)			Value (000)			Unrealized Appreciation (Depreciation) (000)
Long:
U.S. Treasury 2 yr. Note		306	Dec-20	$	61,200		$	67,614		$	33
U.S. Treasury 5 yr. Note		557	Dec-20		55,700			70,200			143
U.S. Treasury Long Bond		26	Dec-20		2,600			4,583			(21	)
U.S. Treasury Ultra Bond		212	Dec-20		21,200			47,024			32
Short:
Euro OAT		27	Dec-20	EUR	(2,700	)		(5,336	)		(45	)
German Euro 30 yr. Bond		4	Dec-20		(400	)		(1,044	)		(25	)
German Euro Bund		43	Dec-20		(4,300	)		(8,798	)		(56	)
U.S. Treasury 10 yr. Note		43	Dec-20	$	(4,300	)		(6,000	)		(4	)
U.S. Treasury 10 yr. Ultra Long Bond		104	Dec-20		(10,400	)		(16,632	)		(23	)
										$	34

Credit Default Swap Agreements:

The Fund had the following credit default swap agreements open at September 30, 2020:

Swap Counterparty and Reference Obligation	Credit Rating of Reference Obligation†	Buy/Sell Protection	Pay/Receive Fixed Rate			Payment Frequency	Maturity Date	Notional Amount (000)		Value (000)			Upfront Payment Paid (Received) (000)			Unrealized Appreciation (Depreciation) (000)
Morgan Stanley & Co. LLC*  CDX.NA.HY.33	NR	Buy		5.00	%	Quarterly	12/20/24	$	8,500	$	(449	)	$	(699	)	$	250
Morgan Stanley & Co. LLC*  CDX.NA.HY.34	NR	Buy		5.00		Quarterly	6/20/25		6,256		(297	)		87			(384	)
										$	(746	)	$	(612	)	$	(134	)

The accompanying notes are an integral part of the financial statements.
18

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Core Plus Fixed Income Portfolio

@  —  Value is less than $500.

†  —  Credit rating as issued by Standard & Poor's.

*  —  Cleared swap agreement, the broker is Morgan Stanley & Co., LLC.

NR  —  Not Rated.

OAT  —  Obligations Assimilables du Trésor (Treasury Obligation).

AUD  —  Australian Dollar

CAD  —  Canadian Dollar

EGP  —  Egyptian Pound

EUR  —  Euro

GBP  —  British Pound

IDR  —  Indonesian Rupiah

MXN  —  Mexican Peso

NOK  —  Norwegian Krone

NZD  —  New Zealand Dollar

PLN  —  Polish Zloty

RUB  —  Russian Ruble

USD  —  United States Dollar

ZAR  —  South African Rand

Portfolio Composition**

Classification	Percentage of Total Investments
Agency Fixed Rate Mortgages		19.9	%
Industrials		16.6
Short-Term Investments		15.3
Finance		12.3
Other***		10.7
Asset-Backed Securities		10.6
Mortgages — Other		8.2
Sovereign		6.4
Total Investments		100.0	%****

**  Percentages indicated are based upon total investments (excluding Securities held as Collateral on Loaned Securities) as of September 30, 2020.

***  Industries and/or investment types representing less than 5% of total investments.

****  Does not include open long/short futures contracts with a value of approximately $227,231,000 and net unrealized appreciation of approximately $34,000. Does not include open foreign currency forward exchange contracts with net unrealized appreciation of approximately $137,000 and does not include open swap agreements with net unrealized depreciation of approximately $134,000.

The accompanying notes are an integral part of the financial statements.
19

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Core Plus Fixed Income Portfolio

Statement of Assets and Liabilities	September 30, 2020 (000)
Assets:
Investments in Securities of Unaffiliated Issuers, at Value(1) (Cost $866,209)	$	885,841
Investment in Security of Affiliated Issuer, at Value (Cost $160,007)		160,007
Total Investments in Securities, at Value (Cost $1,026,216)		1,045,848
Foreign Currency, at Value (Cost $106)		105
Interest Receivable		4,197
Receivable for Variation Margin on Futures Contracts		2,516
Receivable for Fund Shares Sold		1,608
Receivable for Investments Sold		1,218
Unrealized Appreciation on Foreign Currency Forward Exchange Contracts		806
Tax Reclaim Receivable		11
Receivable from Affiliate		2
Receivable from Securities Lending Income		1
Other Assets		128
Total Assets		1,056,440
Liabilities:
Payable for Investments Purchased		147,849
Collateral on Securities Loaned, at Value		5,536
Payable for Fund Shares Redeemed		1,243
Unrealized Depreciation on Foreign Currency Forward Exchange Contracts		669
Due to Broker		270
Payable for Advisory Fees		239
Payable for Sub Transfer Agency Fees — Class I		82
Payable for Sub Transfer Agency Fees — Class A		21
Payable for Sub Transfer Agency Fees — Class L		—	@
Payable for Sub Transfer Agency Fees — Class C		2
Deferred Capital Gain Country Tax		90
Payable for Professional Fees		77
Payable for Administration Fees		59
Payable for Shareholder Services Fees — Class A		23
Payable for Distribution and Shareholder Services Fees — Class L		—	@
Payable for Distribution and Shareholder Services Fees — Class C		20
Payable for Custodian Fees		25
Payable for Transfer Agency Fees — Class I		3
Payable for Transfer Agency Fees — Class A		1
Payable for Transfer Agency Fees — Class L		—	@
Payable for Transfer Agency Fees — Class C		1
Payable for Transfer Agency Fees — Class IS		1
Payable for Variation Margin on Swap Agreements		3
Other Liabilities		63
Total Liabilities		156,277
Net Assets	$	900,163
Net Assets Consist of:
Paid-in-Capital	$	852,762
Total Distributable Earnings		47,401
Net Assets	$	900,163

The accompanying notes are an integral part of the financial statements.
20

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Core Plus Fixed Income Portfolio

Statement of Assets and Liabilities (cont'd)	September 30, 2020 (000)
CLASS I:
Net Assets	$	662,724
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		55,635,559
Net Asset Value, Offering and Redemption Price Per Share	$	11.91
CLASS A:
Net Assets	$	114,387
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		9,589,291
Net Asset Value, Redemption Price Per Share	$	11.93
Maximum Sales Load		3.25	%
Maximum Sales Charge	$	0.40
Maximum Offering Price Per Share	$	12.33
CLASS L:
Net Assets	$	812
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		67,955
Net Asset Value, Offering and Redemption Price Per Share	$	11.94
CLASS C:
Net Assets	$	25,989
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		2,194,670
Net Asset Value, Offering and Redemption Price Per Share	$	11.84
CLASS IS:
Net Assets	$	96,251
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		8,084,816
Net Asset Value, Offering and Redemption Price Per Share	$	11.91
(1) Including: Securities on Loan, at Value:	$	6,455

@  Amount is less than $500.

The accompanying notes are an integral part of the financial statements.
21

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Core Plus Fixed Income Portfolio

Statement of Operations	Year Ended September 30, 2020 (000)
Investment Income:
Interest from Securities of Unaffiliated Issuers (Net of $72 of Foreign Taxes Withheld)	$	23,074
Dividends from Security of Affiliated Issuer (Note G)		560
Dividends from Securities of Unaffiliated Issuers		39
Income from Securities Loaned — Net		19
Total Investment Income		23,692
Expenses:
Advisory Fees (Note B)		2,934
Sub Transfer Agency Fees — Class I		604
Sub Transfer Agency Fees — Class A		140
Sub Transfer Agency Fees — Class L		—	@
Sub Transfer Agency Fees — Class C		12
Administration Fees (Note C)		626
Shareholder Services Fees — Class A (Note D)		260
Distribution and Shareholder Services Fees — Class L (Note D)		4
Distribution and Shareholder Services Fees — Class C (Note D)		198
Registration Fees		169
Professional Fees		153
Custodian Fees (Note F)		98
Pricing Fees		85
Shareholder Reporting Fees		64
Transfer Agency Fees — Class I (Note E)		9
Transfer Agency Fees — Class A (Note E)		5
Transfer Agency Fees — Class L (Note E)		2
Transfer Agency Fees — Class C (Note E)		4
Transfer Agency Fees — Class IS (Note E)		2
Trustees' Fees and Expenses		14
Other Expenses		43
Expenses Before Non Operating Expenses		5,426
Bank Overdraft Expense		4
Total Expenses		5,430
Waiver of Advisory Fees (Note B)		(1,289	)
Reimbursement of Class Specific Expenses — Class I (Note B)		(326	)
Reimbursement of Class Specific Expenses — Class L (Note B)		(1	)
Reimbursement of Class Specific Expenses — Class IS (Note B)		(2	)
Rebate from Morgan Stanley Affiliate (Note G)		(153	)
Net Expenses		3,659
Net Investment Income		20,033
Realized Gain (Loss):
Investments Sold (Net of $36 of Capital Gain Country Tax)		25,672
Foreign Currency Forward Exchange Contracts		(1,592	)
Foreign Currency Translation		(132	)
Futures Contracts		2,428
Swap Agreements		1,009
Net Realized Gain		27,385
Change in Unrealized Appreciation (Depreciation):
Investments (Net of Decrease in Deferred Capital Gain Country Tax of $38)		(123	)
Foreign Currency Forward Exchange Contracts		(497	)
Foreign Currency Translation		16
Futures Contracts		254
Swap Agreements		(134	)
Net Change in Unrealized Appreciation (Depreciation)		(484	)
Net Realized Gain and Change in Unrealized Appreciation (Depreciation)		26,901
Net Increase in Net Assets Resulting from Operations	$	46,934

@  Amount is less than $500.

The accompanying notes are an integral part of the financial statements.
22

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Core Plus Fixed Income Portfolio

Statements of Changes in Net Assets	Year Ended September 30, 2020 (000)			Year Ended September 30, 2019 (000)
Increase (Decrease) in Net Assets:
Operations:
Net Investment Income	$	20,033		$	13,332
Net Realized Gain		27,385			3,415
Net Change in Unrealized Appreciation (Depreciation)		(484	)		26,965
Net Increase in Net Assets Resulting from Operations		46,934			43,712
Dividends and Distributions to Shareholders:
Class I		(18,149	)		(11,689	)
Class A		(2,980	)		(2,538	)
Class L		(20	)		(17	)
Class C		(432	)		(229	)
Class IS		(2,603	)		(—	@)
Total Dividends and Distributions to Shareholders		(24,184	)		(14,473	)
Capital Share Transactions:(1)
Class I:
Subscribed		449,352			258,962
Distributions Reinvested		17,870			11,394
Redeemed		(278,475	)		(93,324	)
Class A:
Subscribed		59,971			57,507
Distributions Reinvested		2,980			2,538
Redeemed		(43,470	)		(39,054	)
Class L:
Exchanged		73			341
Distributions Reinvested		20			17
Redeemed		(24	)		(150	)
Class C:
Subscribed		15,394			9,758
Distributions Reinvested		427			225
Redeemed		(5,020	)		(2,836	)
Class IS:
Subscribed		102,407			—
Distributions Reinvested		2,250			—	@
Redeemed		(11,558	)		—
Net Increase in Net Assets Resulting from Capital Share Transactions		312,197			205,378
Total Increase in Net Assets		334,947			234,617
Net Assets:
Beginning of Period		565,216			330,599
End of Period	$	900,163		$	565,216

The accompanying notes are an integral part of the financial statements.
23

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Core Plus Fixed Income Portfolio

Statements of Changes in Net Assets (cont'd)	Year Ended September 30, 2020 (000)			Year Ended September 30, 2019 (000)
(1)   Capital Share Transactions:
Class I:
Shares Subscribed		38,635			23,170
Shares Issued on Distributions Reinvested		1,542			1,028
Shares Redeemed		(24,048	)		(8,452	)
Net Increase in Class I Shares Outstanding		16,129			15,746
Class A:
Shares Subscribed		5,160			5,169
Shares Issued on Distributions Reinvested		257			229
Shares Redeemed		(3,776	)		(3,499	)
Net Increase in Class A Shares Outstanding		1,641			1,899
Class L:
Shares Exchanged		6			31
Shares Issued on Distributions Reinvested		2			2
Shares Redeemed		(2	)		(14	)
Net Increase in Class L Shares Outstanding		6			19
Class C:
Shares Subscribed		1,325			873
Shares Issued on Distributions Reinvested		37			20
Shares Redeemed		(442	)		(256	)
Net Increase in Class C Shares Outstanding		920			637
Class IS:
Shares Subscribed		8,888			—
Shares Issued on Distributions Reinvested		194			—	@@
Shares Redeemed		(998	)		—
Net Increase in Class IS Shares Outstanding		8,084			—	@@

@  Amount is less than $500.

@@  Amount is less than 500 shares.

The accompanying notes are an integral part of the financial statements.
24

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Core Plus Fixed Income Portfolio

	Class I
	Year Ended September 30,
Selected Per Share Data and Ratios	2020			2019			2018			2017			2016(1)
Net Asset Value, Beginning of Period	$	11.58		$	10.84		$	11.17		$	11.22		$	10.18
Income (Loss) from Investment Operations:
Net Investment Income(2)		0.31			0.37			0.34			0.32			0.34
Net Realized and Unrealized Gain (Loss)		0.40			0.78			(0.38	)		(0.02	)		1.11
Total from Investment Operations		0.71			1.15			(0.04	)		0.30			1.45
Distributions from and/or in Excess of:
Net Investment Income		(0.30	)		(0.41	)		(0.29	)		(0.35	)		(0.41	)
Net Realized Gain		(0.08	)		—			—			—			—
Total Distributions		(0.38	)		(0.41	)		(0.29	)		(0.35	)		(0.41	)
Net Asset Value, End of Period	$	11.91		$	11.58		$	10.84		$	11.17		$	11.22
Total Return(3)		6.27	%		10.83	%(4)		(0.36	)%		2.79	%(5)		14.80	%(6)
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	662,724		$	457,610		$	257,605		$	265,958		$	193,976
Ratio of Expenses Before Expense Limitation		0.64	%		0.67	%		0.70	%		0.73	%		0.74	%
Ratio of Expenses After Expense Limitation		0.40	%(7)		0.41	%(7)		0.40	%(7)		0.40	%(7)		0.43	%(7)(8)
Ratio of Expenses After Expense Limitation Excluding Non-Operating Expenses		0.40	%(7)		N/A			N/A			N/A			N/A
Ratio of Net Investment Income		2.63	%(7)		3.29	%(7)		3.09	%(7)		2.94	%(7)		3.31	%(7)(8)
Ratio of Rebate from Morgan Stanley Affiliates		0.02	%		0.01	%		0.02	%		0.02	%		0.01	%
Portfolio Turnover Rate		287	%		217	%		248	%		350	%		262	%

(1)  Reflects prior period custodian out-of-pocket expenses that were reimbursed in September 2016. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class I shares. The Ratio of Expenses After Expense Limitation and the Ratio of Net Investment Income would be unchanged as the reimbursement of custodian fees was offset against expense waivers/reimbursements with no impact to net expenses or net investment income.

(2)  Per share amount is based on average shares outstanding.

(3)  Calculated based on the net asset value as of the last business day of the period.

(4)  Performance was positively impacted by approximately 0.20% due to the receipt of proceeds from the settlement of a class action suit involving the Fund's past holdings. This was a one-time settlement, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had this settlement not occurred, the total return for Class I shares would have been approximately 10.63%.

(5)  Performance was positively impacted by approximately 0.46% due to the receipt of proceeds from the settlement of class action suits involving the Fund's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class I shares would have been approximately 2.33%.

(6)  Performance was positively impacted by approximately 7.72% due to the receipt of proceeds from the settlement of class action suits involving the Fund's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class I shares would have been approximately 7.08%.

(7)  The Ratio of Expenses After Expense Limitation and Ratio of Net Investment Income reflect the rebate of certain Fund expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates."

(8)  Effective January 4, 2016, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 0.42% for Class I shares. Prior to January 4, 2016, the maximum ratio was 0.52% for Class I shares.

The accompanying notes are an integral part of the financial statements.
25

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Core Plus Fixed Income Portfolio

	Class A
	Year Ended September 30,
Selected Per Share Data and Ratios	2020			2019			2018			2017			2016(1)
Net Asset Value, Beginning of Period	$	11.60		$	10.85		$	11.18		$	11.23		$	10.19
Income (Loss) from Investment Operations:
Net Investment Income(2)		0.27			0.33			0.30			0.28			0.30
Net Realized and Unrealized Gain (Loss)		0.40			0.79			(0.38	)		(0.02	)		1.12
Total from Investment Operations		0.67			1.12			(0.08	)		0.26			1.42
Distributions from and/or in Excess of:
Net Investment Income		(0.26	)		(0.37	)		(0.25	)		(0.31	)		(0.38	)
Net Realized Gain		(0.08	)		—			—			—			—
Total Distributions		(0.34	)		(0.37	)		(0.25	)		(0.31	)		(0.38	)
Net Asset Value, End of Period	$	11.93		$	11.60		$	10.85		$	11.18		$	11.23
Total Return(3)		5.91	%		10.49	%(4)		(0.70	)%		2.43	%(5)		14.31	%(6)
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	114,387		$	92,191		$	65,647		$	60,874		$	24,071
Ratio of Expenses Before Expense Limitation		0.92	%		0.97	%		1.00	%		1.02	%		1.15	%
Ratio of Expenses After Expense Limitation		0.74	%(7)		0.75	%(7)		0.75	%(7)		0.75	%(7)		0.76	%(7)(8)
Ratio of Expenses After Expense Limitation Excluding Non-Operating Expenses		0.74	%(7)		N/A			N/A			N/A			N/A
Ratio of Net Investment Income		2.29	%(7)		2.96	%(7)		2.73	%(7)		2.58	%(7)		2.82	%(7)(8)
Ratio of Rebate from Morgan Stanley Affiliates		0.02	%		0.01	%		0.02	%		0.02	%		0.02	%
Portfolio Turnover Rate		287	%		217	%		248	%		350	%		262	%

(1)  Reflects prior period custodian out-of-pocket expenses that were reimbursed in September 2016. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class A shares. The Ratio of Expenses After Expense Limitation and the Ratio of Net Investment Income would be unchanged as the reimbursement of custodian fees was offset against expense waivers/reimbursements with no impact to net expenses or net investment income.

(2)  Per share amount is based on average shares outstanding.

(3)  Calculated based on the net asset value which does not reflect sales charges, if applicable, as of the last business day of the period.

(4)  Performance was positively impacted by approximately 0.20% due to the receipt of proceeds from the settlement of a class action suit involving the Fund's past holdings. This was a one-time settlement, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had this settlement not occurred, the total return for Class A shares would have been approximately 10.29%.

(5)  Performance was positively impacted by approximately 0.46% due to the receipt of proceeds from the settlement of class action suits involving the Fund's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class A shares would have been approximately 1.97%.

(6)  Performance was positively impacted by approximately 7.76% due to the receipt of proceeds from the settlement of class action suits involving the Fund's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class A shares would have been approximately 6.55%.

(7)  The Ratio of Expenses After Expense Limitation and Ratio of Net Investment Income reflect the rebate of certain Fund expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates."

(8)  Effective January 4, 2016, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 0.77% for Class A shares. Prior to January 4, 2016, the maximum ratio was 0.87% for Class A shares.

The accompanying notes are an integral part of the financial statements.
26

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Core Plus Fixed Income Portfolio

	Class L
	Year Ended September 30,
Selected Per Share Data and Ratios	2020			2019			2018			2017			2016(1)
Net Asset Value, Beginning of Period	$	11.61		$	10.86		$	11.17		$	11.23		$	10.18
Income (Loss) from Investment Operations:
Net Investment Income(2)		0.24			0.30			0.27			0.26			0.28
Net Realized and Unrealized Gain (Loss)		0.40			0.78			(0.37	)		(0.03	)		1.12
Total from Investment Operations		0.64			1.08			(0.10	)		0.23			1.40
Distributions from and/or in Excess of:
Net Investment Income		(0.23	)		(0.33	)		(0.21	)		(0.29	)		(0.35	)
Net Realized Gain		(0.08	)		—			—			—			—
Total Distributions		(0.31	)		(0.33	)		(0.21	)		(0.29	)		(0.35	)
Net Asset Value, End of Period	$	11.94		$	11.61		$	10.86		$	11.17		$	11.23
Total Return(3)		5.63	%		10.12	%(4)		(0.95	)%		2.16	%(5)		14.10	%(6)
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	812		$	720		$	464		$	1,138		$	841
Ratio of Expenses Before Expense Limitation		1.37	%		1.45	%		1.41	%		1.35	%		1.82	%
Ratio of Expenses After Expense Limitation		1.00	%(7)		1.01	%(7)		1.00	%(7)		1.00	%(7)		1.03	%(7)(8)
Ratio of Expenses After Expense Limitation Excluding Non-Operating Expenses		1.00	%(7)		N/A			N/A			N/A			N/A
Ratio of Net Investment Income		2.04	%(7)		2.70	%(7)		2.46	%(7)		2.37	%(7)		2.65	%(7)(8)
Ratio of Rebate from Morgan Stanley Affiliates		0.02	%		0.01	%		0.02	%		0.02	%		0.01	%
Portfolio Turnover Rate		287	%		217	%		248	%		350	%		262	%

(1)  Reflects prior period custodian out-of-pocket expenses that were reimbursed in September 2016. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class L shares. The Ratio of Expenses After Expense Limitation and the Ratio of Net Investment Income would be unchanged as the reimbursement of custodian fees was offset against expense waivers/reimbursements with no impact to net expenses or net investment income.

(2)  Per share amount is based on average shares outstanding.

(3)  Calculated based on the net asset value as of the last business day of the period.

(4)  Performance was positively impacted by approximately 0.20% due to the receipt of proceeds from the settlement of a class action suit involving the Fund's past holdings. This was a one-time settlement, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had this settlement not occurred, the total return for Class L shares would have been approximately 9.92%.

(5)  Performance was positively impacted by approximately 0.46% due to the receipt of proceeds from the settlement of class action suits involving the Fund's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class L shares would have been approximately 1.70%.

(6)  Performance was positively impacted by approximately 7.76% due to the receipt of proceeds from the settlement of class action suits involving the Fund's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class L shares would have been approximately 6.34%.

(7)  The Ratio of Expenses After Expense Limitation and Ratio of Net Investment Income reflect the rebate of certain Fund expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates."

(8)  Effective January 4, 2016, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 1.02% for Class L shares. Prior to January 4, 2016, the maximum ratio was 1.12% for Class L shares.

The accompanying notes are an integral part of the financial statements.
27

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Core Plus Fixed Income Portfolio

	Class C
	Year Ended September 30,
Selected Per Share Data and Ratios	2020			2019			2018			2017			2016(1)
Net Asset Value, Beginning of Period	$	11.52		$	10.77		$	11.10		$	11.17		$	10.16
Income (Loss) from Investment Operations:
Net Investment Income(2)		0.18			0.25			0.22			0.20			0.22
Net Realized and Unrealized Gain (Loss)		0.41			0.78			(0.37	)		(0.03	)		1.12
Total from Investment Operations		0.59			1.03			(0.15	)		0.17			1.34
Distributions from and/or in Excess of:
Net Investment Income		(0.19	)		(0.28	)		(0.18	)		(0.24	)		(0.33	)
Net Realized Gain		(0.08	)		—			—			—			—
Total Distributions		(0.27	)		(0.28	)		(0.18	)		(0.24	)		(0.33	)
Net Asset Value, End of Period	$	11.84		$	11.52		$	10.77		$	11.10		$	11.17
Total Return(3)		5.16	%		9.70	%(4)		(1.39	)%		1.57	%(5)		13.52	%(6)
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	25,989		$	14,684		$	6,873		$	4,890		$	3,528
Ratio of Expenses Before Expense Limitation		1.62	%		1.68	%		1.73	%		1.74	%		2.00	%
Ratio of Expenses After Expense Limitation		1.43	%(7)		1.46	%(7)		1.50	%(7)		1.50	%(7)		1.51	%(7)(8)
Ratio of Expenses After Expense Limitation Excluding Non-Operating Expenses		1.43	%(7)		N/A			N/A			N/A			N/A
Ratio of Net Investment Income		1.60	%(7)		2.23	%(7)		2.01	%(7)		1.86	%(7)		2.04	%(7)(8)
Ratio of Rebate from Morgan Stanley Affiliates		0.02	%		0.01	%		0.02	%		0.02	%		0.02	%
Portfolio Turnover Rate		287	%		217	%		248	%		350	%		262	%

(1)  Reflects prior period custodian out-of-pocket expenses that were reimbursed in September 2016. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class C shares. The Ratio of Expenses After Expense Limitation and the Ratio of Net Investment Income would be unchanged as the reimbursement of custodian fees was offset against expense waivers/reimbursements with no impact to net expenses or net investment income.

(2)  Per share amount is based on average shares outstanding.

(3)  Calculated based on the net asset value which does not reflect sales charges, if applicable, as of the last business day of the period.

(4)  Performance was positively impacted by approximately 0.20% due to the receipt of proceeds from the settlement of a class action suit involving the Fund's past holdings. This was a one-time settlement, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had this settlement not occurred, the total return for Class C shares would have been approximately 9.50%.

(5)  Performance was positively impacted by approximately 0.46% due to the receipt of proceeds from the settlement of class action suits involving the Fund's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class C shares would have been approximately 1.11%.

(6)  Performance was positively impacted by approximately 7.75% due to the receipt of proceeds from the settlement of class action suits involving the Fund's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class C shares would have been approximately 5.77%.

(7)  The Ratio of Expenses After Expense Limitation and Ratio of Net Investment Income reflect the rebate of certain Fund expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates."

(8)  Effective January 4, 2016, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 1.52% for Class C shares. Prior to January 4, 2016, the maximum ratio was 1.62% for Class C shares.

The accompanying notes are an integral part of the financial statements.
28

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Core Plus Fixed Income Portfolio

	Class IS
	Year Ended September 30,						Period from June 15, 2018(1) to
Selected Per Share Data and Ratios	2020			2019			September 30, 2018
Net Asset Value, Beginning of Period	$	11.58		$	10.84		$	10.85
Income (Loss) from Investment Operations:
Net Investment Income(2)		0.31			0.37			0.10
Net Realized and Unrealized Gain (Loss)		0.41			0.78			(0.04	)
Total from Investment Operations		0.72			1.15			0.06
Distributions from and/or in Excess of:
Net Investment Income		(0.31	)		(0.41	)		(0.07	)
Net Realized Gain		(0.08	)		—			—
Total Distributions		(0.39	)		(0.41	)		(0.07	)
Net Asset Value, End of Period	$	11.91		$	11.58		$	10.84
Total Return(3)		6.24	%		10.89	%(4)		0.56	%(6)
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	96,251		$	11		$	10
Ratio of Expenses Before Expense Limitation		0.54	%		18.96	%		18.71	%(7)
Ratio of Expenses After Expense Limitation		0.35	%(5)		0.35	%(5)		0.35	%(5)(7)
Ratio of Expenses After Expense Limitation Excluding Non-Operating Expenses		0.35	%(5)		N/A			N/A
Ratio of Net Investment Income		2.67	%(5)		3.33	%(5)		3.17	%(5)(7)
Ratio of Rebate from Morgan Stanley Affiliates		0.02	%		0.01	%		0.02	%(7)
Portfolio Turnover Rate		287	%		217	%		248	%(6)

(1)  Commencement of Offering.

(2)  Per share amount is based on average shares outstanding.

(3)  Calculated based on the net asset value as of the last business day of the period.

(4)  Performance was positively impacted by approximately 0.20% due to the receipt of proceeds from the settlement of a class action suit involving the Fund's past holdings. This was a one-time settlement, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had this settlement not occurred, the total return for Class IS shares would have been approximately 10.69%.

(5)  The Ratio of Expenses After Expense Limitation and Ratio of Net Investment Income reflect the rebate of certain Fund expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates."

(6)  Not annualized.

(7)  Annualized.

The accompanying notes are an integral part of the financial statements.
29

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements

Morgan Stanley Institutional Fund Trust ("Trust'') is registered under the Investment Company Act of 1940, as amended (the "Act''), as an open-end management investment company. The Trust is comprised of twelve separate, active funds (individually referred to as a "Fund," collectively as the "Funds"). The Trust applies investment company accounting and reporting guidance. All Funds are considered diversified for purposes of the Act.

The accompanying financial statements relate to the Core Plus Fixed Income Portfolio. The Fund seeks above-average total return over a market cycle of three to five years. The Fund offers five classes of shares — Class I, Class A, Class L, Class C and Class IS.

The Fund has suspended offering Class L shares for sale to all investors. Class L shareholders of the Fund do not have the option of purchasing additional Class L shares. However, existing Class L shareholders may invest in additional Class L shares through reinvestment of dividends and distributions.

A. Significant Accounting Policies: The following significant accounting policies are in conformity with U.S. generally accepted accounting principles ("GAAP"). Such policies are consistently followed by the Trust in the preparation of its financial statements. GAAP may require management to make estimates and assumptions that affect the reported amounts and disclosures in the financial statements. Actual results may differ from those estimates.

In March 2017, the Financial Accounting Standards Board ("FASB") issued an Accounting Standard Update, ASU 2017-08, Receivables-Nonrefundable Fees and Other Costs (Subtopic 310-20), Premium Amortization on Purchased Callable Debt Securities ("ASU 2017-08") which amends the amortization period for certain purchased callable debt securities held at a premium, shortening such period to the earliest call date. ASU 2017-08 does not require any accounting change for debt securities held at a discount; the discount continues to be accreted to maturity. ASU 2017-08 is effective for fiscal years, and interim periods within those fiscal years, beginning after December 15, 2018. The adoption resulted in a change in accounting principle, since the Fund had historically amortized such premiums to maturity for U.S. GAAP. Accordingly, the Fund has adopted ASU 2017-08 to amend the premium amortization period for certain purchased callable debt securities with non-contingent call features to the earliest call date. It is impracticable to evaluate the effect on individual prior periods, therefore the Fund applied the amendments on a modified retrospective basis by recognizing a cumulative effect

adjustment that decreased the beginning of period cost of investments and increased the unrealized appreciation on investments of approximately $5,000.

This change in accounting policy has been made to comply with the newly issued accounting standard and had no impact on total accumulated earnings (loss) or the net asset value of the Fund. With respect to the Fund's results of operations, amortization of premium to first call date accelerates amortization with the intent of more closely aligning the recognition of income on such bonds with the economics of the instrument.

In March 2020, FASB issued an Accounting Standard Update, ASU 2020-04, Reference Rate Reform (Topic 848) — Facilitation of the Effects of Reference Rate Reform on Financial Reporting ("ASU 2020-04"), which provides optional, temporary relief with respect to the financial reporting of contracts subject to certain types of modifications due to the planned discontinuation of the London Interbank Offered Rate ("LIBOR") and other IBOR-based reference rates at the end of 2021. The temporary relief provided by ASU 2020-04 is effective for certain reference rate-related contract modifications that occur during the period from March 12, 2020 through December 31, 2022. Management is evaluating the impact of ASU 2020-04 on the Fund's investments, derivatives, debt and other contracts that will undergo reference rate-related modifications as a result of the reference rate reform.

1.  Security Valuation: (1) Certain portfolio securities may be valued by an outside pricing service/vendor approved by the Trust's Board of Trustees (the "Trustees"). The pricing service/vendor may employ a pricing model that takes into account, among other things, bids, yield spreads and/or other market data and specific security characteristics. Alternatively, if a valuation is not available from an outside pricing service/vendor, and the security trades on an exchange, the security may be valued at its latest reported sale price (or at the exchange official closing price if such exchange reports an official closing price), prior to the time when assets are valued. If there are no sales on a given day and if there is no official exchange closing price for that day, the security is valued at the mean between the last reported bid and asked prices if such bid and asked prices are available in the relevant exchanges. If only bid prices are available then the latest bid price may be used. If Morgan Stanley Investment Management Inc. (the "Adviser"), a wholly-owned subsidiary of Morgan Stanley, determines that the price provided by the outside pricing service/vendor or exchange does not reflect the security's

30

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

fair value or is unable to provide a price, prices from brokers or dealers may also be utilized. In these circumstances, the value of the security will be the mean of bid and asked prices obtained from brokers or dealers; (2) futures are valued at the settlement price on the exchange on which they trade or, if a settlement price is unavailable, at the last sale price on the exchange; (3) over-the-counter ("OTC") swaps may be valued by an outside pricing service approved by the Trustees or quotes from a broker or dealer. Swaps cleared on a clearinghouse or exchange may be valued using the closing price provided by the clearinghouse or exchange; (4) when market quotations are not readily available, including circumstances under which the Adviser determines that the closing price, last sale price or the mean between the last reported bid and asked prices are not reflective of a security's market value, portfolio securities are valued at their fair value as determined in good faith under procedures established by and under the general supervision of the Trustees. Occasionally, developments affecting the closing prices of securities and other assets may occur between the times at which valuations of such securities are determined (that is, close of the foreign market on which the securities trade) and the close of business of the New York Stock Exchange ("NYSE"). If developments occur during such periods that are expected to materially affect the value of such securities, such valuations may be adjusted to reflect the estimated fair value of such securities as of the close of the NYSE, as determined in good faith by the Trustees or by the Adviser using a pricing service and/or procedures approved by the Trustees; (5) quotations of foreign portfolio securities, other assets and liabilities and forward contracts stated in foreign currency are translated into U.S. dollar equivalents at the prevailing market rates prior to the close of the NYSE; and (6) investments in mutual funds, including the Morgan Stanley Institutional Liquidity Funds, are valued at the net asset value ("NAV") as of the close of each business day.

The Trustees have responsibility for determining in good faith the fair value of the investments, and the Trustees may appoint others, such as the Trust's Adviser or a valuation committee, to assist the Trustees in determining fair value and to make the actual calculations pursuant to the fair valuation methodologies previously approved by the Trustees. Under procedures approved by the Trustees, the Trust's Adviser has formed a Valuation Committee whose members are approved by the

Trustees. The Valuation Committee provides administration and oversight of the Trust's valuation policies and procedures, which are reviewed at least annually by the Trustees. These procedures allow the Trust to utilize independent pricing services, quotations from securities and financial instrument dealers and other market sources to determine fair value.

2.  Fair Value Measurement: FASB Accounting Standards Codification^TM ("ASC") 820, "Fair Value Measurement" ("ASC 820"), defines fair value as the value that the Fund would receive to sell an investment or pay to transfer a liability in a timely transaction with an independent buyer in the principal market, or in the absence of a principal market, the most advantageous market for the investment or liability. ASC 820 establishes a three-tier hierarchy to distinguish between (1) inputs that reflect the assumptions market participants would use in valuing an asset or liability developed based on market data obtained from sources independent of the reporting entity (observable inputs) and (2) inputs that reflect the reporting entity's own assumptions about the assumptions market participants would use in valuing an asset or liability developed based on the best information available in the circumstances (unobservable inputs) and to establish classification of fair value measurements for disclosure purposes. Various inputs are used in determining the value of the Fund's investments. The inputs are summarized in the three broad levels listed below:

•  Level 1 – unadjusted quoted prices in active markets for identical investments

•  Level 2 – other significant observable inputs (including quoted prices for similar investments, interest rates, prepayment speeds, credit risk, etc.)

•  Level 3 – significant unobservable inputs including the Fund's own assumptions in determining the fair value of investments. Factors considered in making this determination may include, but are not limited to, information obtained by contacting the issuer, analysts, or the appropriate stock exchange (for exchange-traded securities), analysis of the issuer's financial statements or other available documents and, if necessary, available information concerning other securities in similar circumstances.

31

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

The inputs or methodology used for valuing securities are not necessarily an indication of the risk associated with investing in those securities and the determination of the significance of a particular input to the fair value measurement in its entirety requires judgment and considers factors specific to each security.

The following is a summary of the inputs used to value the Fund's investments as of September 30, 2020:

Investment Type	Level 1 Unadjusted quoted prices (000)			Level 2 Other significant observable inputs (000)			Level 3 Significant unobservable inputs (000)		Total (000)
Assets:
Fixed Income Securities
Agency Adjustable Rate Mortgage	$	—		$	54		$	—	$	54
Agency Fixed Rate Mortgages		—			207,392			—		207,392
Asset-Backed Securities		—			110,282			—		110,282
Collateralized Mortgage Obligations — Agency Collateral Series		—			3,964			—		3,964
Commercial Mortgage- Backed Securities		—			45,986			—		45,986
Corporate Bonds		—			323,834			—		323,834
Mortgages — Other		—			85,541			—		85,541
Municipal Bonds		—			10,655			—		10,655
Sovereign		—			66,497			—		66,497
U.S. Treasury Security		—			10,656			—		10,656
Variable Rate Senior Loan Interests		—			16,150			—		16,150
Total Fixed Income Securities		—			881,011			—		881,011
Short-Term Investments
Investment Company		160,007			—			—		160,007
Sovereign		—			2,313			—		2,313
U.S. Treasury Securities		—			2,517			—		2,517
Total Short-Term Investments		160,007			4,830			—		164,837
Foreign Currency Forward Exchange Contracts		—			806			—		806
Futures Contracts		208			—			—		208
Credit Default Swap Agreement		—			250			—		250
Total Assets		160,215			886,897			—		1,047,112
Liabilities:
Foreign Currency Forward Exchange Contracts		—			(669	)		—		(669	)
Futures Contracts		(174	)		—			—		(174	)
Credit Default Swap Agreement		—			(384	)		—		(384	)
Total Liabilities		(174	)		(1,053	)		—		(1,227	)
Total	$	160,041		$	885,844		$	—	$	1,045,885

Transfers between investment levels may occur as the markets fluctuate and/or the availability of data used in an investment's valuation changes.

3.  Foreign Currency Translation and Foreign Investments: The books and records of the Fund are maintained in U.S. dollars. Foreign currency amounts are translated into U.S. dollars as follows:

–  investments, other assets and liabilities at the prevailing rate of exchange on the valuation date;

–  investment transactions and investment income at the prevailing rates of exchange on the dates of such transactions.

Although the net assets of the Fund are presented at the foreign exchange rates and market values at the close of the period, the Fund does not isolate that portion of the results of operations arising as a result of changes in the foreign exchange rates from the fluctuations arising from changes in the market prices of securities held at period end. Similarly, the Fund does not isolate the effect of changes in foreign exchange rates from the fluctuations arising from changes in the market prices of securities sold during the period. Accordingly, realized and unrealized foreign currency gains (losses) on investments in securities are included in the reported net realized and unrealized gains (losses) on investment transactions and balances. However, pursuant to U.S. federal income tax regulations, gains and losses from certain foreign currency transactions and the foreign currency portion of gains and losses realized on sales and maturities of foreign denominated debt securities are treated as ordinary income for U.S. federal income tax purposes.

Net realized gains (losses) on foreign currency transactions represent net foreign exchange gains (losses) from foreign currency forward exchange contracts, disposition of foreign currencies, currency gains (losses) realized between the trade and settlement dates on securities transactions, and the difference between the amount of investment income and foreign withholding taxes recorded on the Fund's books and the U.S. dollar equivalent amounts actually received or paid. The change in unrealized currency gains (losses) on foreign currency transactions for the period is reflected in the Statement of Operations.

32

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

Foreign security and currency transactions may involve certain considerations and risks not typically associated with those of U.S. dollar denominated transactions as a result of, among other factors, fluctuations of exchange rates in relation to the U.S. dollar, the possibility of lower levels of governmental supervision and regulation of foreign securities markets and the possibility of political or economic instability.

Governmental approval for foreign investments may be required in advance of making an investment under certain circumstances in some countries, and the extent of foreign investments in domestic companies may be subject to limitation in other countries. Foreign ownership limitations also may be imposed by the charters of individual companies to prevent, among other concerns, violations of foreign investment limitations. As a result, an additional class of shares (identified as "Foreign" in the Portfolio of Investments) may be created and offered for investment. The "local" and "foreign shares" market values may differ. In the absence of trading of the foreign shares in such markets, the Fund values the foreign shares at the closing exchange price of the local shares.

4.  Derivatives: The Fund may, but is not required to, use derivative instruments for a variety of purposes, including hedging, risk management, portfolio management or to earn income. Derivatives are financial instruments whose value is based, in part, on the value of an underlying asset, interest rate, index or financial instrument. Prevailing interest rates and volatility levels, among other things, also affect the value of derivative instruments. A derivative instrument often has risks similar to its underlying asset and may have additional risks, including imperfect correlation between the value of the derivative and the underlying asset, risks of default by the counterparty to certain transactions, magnification of losses incurred due to changes in the market value of the securities, instruments, indices or interest rates to which the derivative instrument relates, risks that the transactions may not be liquid and risks arising from margin requirements. The use of derivatives involves risks that are different from, and possibly greater than, the risks associated with other portfolio investments. Derivatives may involve the use of highly specialized instruments that require investment techniques and risk analyses different from those associated with other portfolio investments. All of the Fund's holdings, including derivative instruments, are marked-to-market each day with

the change in value reflected in unrealized appreciation (depreciation). Upon disposition, a realized gain or loss is recognized.

Certain derivative transactions may give rise to a form of leverage. Leverage magnifies the potential for gain and the risk of loss. Leverage associated with derivative transactions may cause the Fund to liquidate portfolio positions when it may not be advantageous to do so to satisfy its obligations or to meet earmarking or segregation requirements, pursuant to applicable Securities and Exchange Commission ("SEC") rules and regulations, or may cause the Fund to be more volatile than if the Fund had not been leveraged. Although the Adviser seeks to use derivatives to further the Fund's investment objectives, there is no assurance that the use of derivatives will achieve this result.

Following is a description of the derivative instruments and techniques that the Fund used during the period and their associated risks:

Futures: A futures contract is a standardized, exchange-traded agreement to buy or sell a specific quantity of an underlying asset, reference rate or index at a specific price at a specific future time. The value of a futures contract tends to increase and decrease in tandem with the value of the underlying instrument. Depending on the terms of the particular contract, futures contracts are settled through either physical delivery of the underlying instrument on the settlement date or by payment of a cash settlement amount on the settlement date. During the period the futures contract is open, payments are received from or made to the broker based upon changes in the value of the contract (the variation margin). A decision as to whether, when and how to use futures contracts involves the exercise of skill and judgment and even a well-conceived futures transaction may be unsuccessful because of market behavior or unexpected events. In addition to the derivatives risks discussed above, the prices of futures contracts can be highly volatile, using futures contracts can lower total return and the potential loss from futures contracts can exceed the Fund's initial investment in such contracts. No assurance can be given that a liquid market will exist for any particular futures contract at any particular time. There is also the risk of loss by the Fund of margin deposits in the event of bankruptcy of a broker with which the Fund has open positions in the futures contract.

33

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

Swaps: The Fund may enter into OTC swap contracts or cleared swap transactions. A swap contract is an agreement between two parties pursuant to which the parties exchange payments at specified dates on the basis of a specified notional amount, with the payments calculated by reference to specified securities, indices, reference rates, currencies or other instruments. Typically swap agreements provide that when the period payment dates for both parties are the same, the payments are made on a net basis (i.e., the two payment streams are netted out, with only the net amount paid by one party to the other). The Fund's obligations or rights under a swap contract entered into on a net basis will generally be equal only to the net amount to be paid or received under the agreement, based on the relative values of the positions held by each party. Cleared swap transactions may help reduce counterparty credit risk. In a cleared swap, the Fund's ultimate counterparty is a clearinghouse rather than a swap dealer, bank or other financial institution. OTC swap agreements are not entered into or traded on exchanges and often there is no central clearing or guaranty function for OTC swaps. These OTC swaps are often subject to credit risk or the risk of default or non-performance by the counterparty. Both OTC and cleared swaps could result in losses if interest rates, foreign currency exchange rates or other factors are not correctly anticipated by the Fund or if the reference index, security or investments do not perform as expected. During the period swap agreements are open, payments are received from or made to the clearinghouse or counterparty based upon changes in the value of the contract (variation margin). The Dodd-Frank Wall Street Reform and Consumer Protection Act and related regulatory developments require the clearing and exchange-trading of certain standardized swap transactions. Mandatory exchange-trading and clearing is occurring on a phased-in basis.

The Fund's use of swaps during the period included those based on the credit of an underlying security commonly referred to as "credit default swaps." The Fund may be either the buyer or seller in a credit default swap. Where the Fund is the buyer of a credit default swap contract, it would typically be entitled to receive the par (or other agreed-upon) value of a referenced debt obligation from the counterparty to the contract only in the event of a default or similar event by the issuer of the

debt obligation. If no default occurs, the Fund would have paid to the counterparty a periodic stream of payments over the term of the contract and received no benefit from the contract. When the Fund is the seller of a credit default swap contract, it typically receives the stream of payments but is obligated to pay an amount equal to the par (or other agreed-upon) value of a referenced debt obligation upon the default or similar event by the issuer of the referenced debt obligation. The use of credit default swaps could result in losses to the Fund if the Adviser fails to correctly evaluate the creditworthiness of the issuer of the referenced debt obligation.

If the Fund is a seller of protection and a credit event occurs, as defined under the terms of that particular swap agreement, the Fund will either (i) pay to the buyer of protection an amount equal to the notional amount of the swap agreement and take delivery of the referenced obligation, other deliverable obligations or underlying securities comprising the referenced index or (ii) pay a net settlement amount in the form of cash or securities equal to the notional amount of the swap agreement less the recovery value of the referenced obligation or underlying securities comprising the referenced index. If the Fund is a buyer of protection and a credit event occurs, as defined under the terms of that particular swap agreement, the Fund will either (i) receive from the seller of protection an amount equal to the notional amount of the swap agreement and deliver the referenced obligation, other deliverable obligations or underlying securities comprising the referenced index or (ii) receive a net settlement amount in the form of cash or securities equal to the notional amount of the swap agreement less the recovery value of the referenced obligation or underlying securities comprising the referenced index. Recovery values are estimated by market makers considering either industry standard recovery rates or entity specific factors and considerations until a credit event occurs. If a credit event has occurred, the recovery value is determined by a facilitated auction whereby a minimum number of allowable broker bids, together with a specified valuation method, are used to calculate the settlement value. The Fund's maximum risk of loss from counterparty risk, either as the protection seller or as the protection buyer, is the fair value of the swap agreement.

34

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

The current credit rating of each individual issuer is listed in the table following the Portfolio of Investments and serves as an indicator of the current status of the payment/performance risk of the credit derivative. Alternatively, for credit default swaps on an index of credits, the quoted market prices and current values serve as an indicator of the current status of the payment/performance risk of the credit derivative. Generally, lower credit ratings and increasing market values, in absolute terms, represent a deterioration of the credit and a greater likelihood of an adverse credit event of the issuer.

When the Fund has an unrealized loss on a swap agreement, the Fund has instructed the custodian to pledge cash or liquid securities as collateral with a value approximately equal to the amount of the unrealized loss. Collateral pledges are monitored and subsequently adjusted if and when the swap valuations fluctuate. If applicable, cash collateral is included with "Due from (to) Broker" in the Statement of Assets and Liabilities.

Upfront payments paid or received by the Fund will be reflected as an asset or liability, respectively, in the Statement of Assets and Liabilities.

Foreign Currency Forward Exchange Contracts: In connection with its investments in foreign securities, the Fund also entered into contracts with banks, brokers or dealers to purchase or sell securities or foreign currencies at a future date. A foreign currency forward exchange contract ("currency contract") is a negotiated agreement between the contracting parties to exchange a specified amount of currency at a specified future time at a specified rate. The rate can be higher or lower than the spot rate between the currencies that are the subject of the contract. Currency contracts may be used to protect against uncertainty in the level of future foreign currency exchange rates or to gain or modify exposure to a particular currency. In addition, the Fund may use cross currency hedging or proxy hedging with respect to currencies in which the Fund has or expects to have portfolio or currency exposure. Cross currency hedges involve the sale of one currency against the positive exposure to a different currency and may be used for hedging purposes or to establish an active exposure to the exchange rate between any two currencies. To the extent hedged by the use of currency contracts, the precise matching of

the currency contract amounts and the value of the securities involved will not generally be possible because the future value of such securities in foreign currencies will change as a consequence of market movements in the value of those securities between the date on which the contract is entered into and the date it matures. Furthermore, such transactions may reduce or preclude the opportunity for gain if the value of the currency should move in the direction opposite to the position taken. There is additional risk to the extent that currency contracts create exposure to currencies in which the Fund's securities are not denominated. Unanticipated changes in currency prices may result in poorer overall performance for the Fund than if it had not entered into such contracts. The use of currency contracts involves the risk of loss from the insolvency or bankruptcy of the counterparty to the contract or the failure of the counterparty to make payments or otherwise comply with the terms of the contract. A currency contract is marked-to-market daily and the change in market value is recorded by the Fund as unrealized gain or loss. The Fund records realized gains (losses) when the currency contract is closed equal to the difference between the value of the currency contract at the time it was opened and the value at the time it was closed.

FASB ASC 815, "Derivatives and Hedging" ("ASC 815"), is intended to improve financial reporting about derivative instruments by requiring enhanced disclosures to enable investors to better understand how and why the Fund uses derivative instruments, how these derivative instruments are accounted for and their effects on the Fund's financial position and results of operations.

The following tables set forth the fair value of the Fund's derivative contracts by primary risk exposure as of September 30, 2020:

	Asset Derivatives Statement of Assets and Liabilities Location	Primary Risk Exposure	Value (000)
Foreign Currency Forward Exchange Contracts	Unrealized Appreciation on Foreign Currency Forward Exchange Contracts	Currency Risk	$	806
Futures Contracts	Variation Margin on Futures Contracts	Interest Rate Risk		208	(a)
Swap Agreements	Variation Margin on Swap Agreement	Credit Risk		250	(a)
Total			$	1,264

35

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

	Liability Derivatives Statement of Assets and Liabilities Location	Primary Risk Exposure	Value (000)
Foreign Currency Forward Exchange Contracts	Unrealized Depreciation on Foreign Currency Forward Exchange Contracts	Currency Risk	$	(669	)
Futures Contracts	Variation Margin on Futures Contracts	Interest Rate Risk		(174	)(a)
Swap Agreements	Variation Margin on Swap Agreement	Credit Risk		(384	)(a)
Total			$	(1,227	)

(a) This amount represents the cumulative appreciation (depreciation) as reported in the Portfolio of Investments. The Statement of Assets and Liabilities only reflects the current day's net variation margin.

The following tables set forth by primary risk exposure the Fund's realized gains (losses) and change in unrealized appreciation (depreciation) by type of derivative contract for the year ended September 30, 2020 in accordance with ASC 815:

Realized Gain (Loss)
Primary Risk Exposure	Derivative Type	Value (000)
Currency Risk	Foreign Currency Forward Exchange Contracts	$	(1,592	)
Interest Rate Risk	Futures Contracts		2,428
Credit Risk	Swap Agreements		1,009
	Total	$	1,845
Change in Unrealized Appreciation (Depreciation)
Primary Risk Exposure	Derivative Type	Value (000)
Currency Risk	Foreign Currency Forward Exchange Contracts	$	(497	)
Interest Rate Risk	Futures Contracts		254
Credit Risk	Swap Agreements		(134	)
	Total	$	(377	)

At September 30, 2020, the Fund's derivative assets and liabilities are as follows:

Gross Amounts of Assets and Liabilities Presented in the Statement of Assets and Liabilities
Derivatives(b)	Assets(c) (000)		Liabilities(c) (000)
Foreign Currency Forward Exchange Contracts	$	806	$	(669	)

(b) Excludes exchange-traded derivatives.

(c) Absent an event of default or early termination, OTC derivative assets and liabilities are presented gross and not offset in the Statement of Assets and Liabilities.

The Fund typically enters into International Swaps and Derivatives Association, Inc. Master Agreements ("ISDA Master Agreements") or similar master agreements (collectively, "Master Agreements") with its contract counterparties for certain OTC derivatives in order to, among other things, reduce its credit risk to counterparties. ISDA Master Agreements include provisions for general obligations, representations, collateral and events

of default or termination. Under an ISDA Master Agreement, the Fund typically may offset with the counterparty certain OTC derivative financial instruments' payables and/or receivables with collateral held and/or posted and create one single net payment (close-out netting) in the event of default, termination and/or potential deterioration in the credit quality of the counterparty. Various Master Agreements govern the terms of certain transactions with counterparties, including transactions such as swap, forward, repurchase and reverse repurchase agreements. These Master Agreements typically attempt to reduce the counterparty risk associated with such transactions by specifying credit protection mechanisms and providing standardization that improves legal certainty. Cross-termination provisions under Master Agreements typically provide that a default in connection with one transaction between the Fund and a counterparty gives the non-defaulting party the right to terminate any other transactions in place with the defaulting party to create one single net payment due to/due from the defaulting party and may be a feature in certain Master Agreements. In the event the Fund exercises its right to terminate a Master Agreement after a counterparty experiences a termination event as defined in the Master Agreement, the return of collateral with market value in excess of the Fund's net liability may be delayed or denied.

The following table presents derivative financial instruments that are subject to enforceable netting arrangements as of September 30, 2020:

Gross Amounts Not Offset in the Statement of Assets and Liabilities
Counterparty	Gross Asset Derivatives Presented in the Statement of Assets and Liabilities (000)		Financial Instrument (000)			Collateral Received (000)(d)			Net Amount (not less than $0) (000)
Australia And New Zealand Banking Group	$	121	$	—		$	—		$	121
Barclays Bank PLC		71		(39	)		—			32
Citibank NA		334		(124	)		(210	)		0
Goldman Sachs International		164		—			—			164
JPMorgan Chase Bank NA		40		(1	)		—			39
UBS AG		76		(76	)		—			0
Total	$	806	$	(240	)	$	(210	)	$	356

(d) In some instances, the actual collateral received may be more than the amount shown here due to overcollateralization.

36

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

Gross Amounts Not Offset in the Statement of Assets and Liabilities
Counterparty	Gross Liability Derivatives Presented in the Statement of Assets and Liabilities (000)		Financial Instrument (000)			Collateral Pledged (000)		Net Amount (not less than $0) (000)
Bank of America NA	$	43	$	—		$	—	$	43
Barclays Bank PLC		39		(39	)		—		0
BNP Paribas SA		149		—			—		149
Citibank NA		124		(124	)		—		0
JPMorgan Chase Bank NA		1		(1	)		—		0
UBS AG		313		(76	)		—		237
Total	$	669	$	(240	)	$	—	$	429

For the year ended September 30, 2020, the approximate average monthly amount outstanding for each derivative type is as follows:

Foreign Currency Forward Exchange Contracts:
Average monthly principal amount	$	124,397,000
Futures Contracts:
Average monthly notional value	$	323,287,000
Swap Agreements:
Average monthly notional amount	$	10,245,000

5.  Securities Lending: The Fund lends securities to qualified financial institutions, such as broker-dealers, to earn additional income. Any increase or decrease in the fair value of the securities loaned that might occur and any interest earned or dividends declared on those securities during the term of the loan would remain in the Fund. The Fund would receive cash or securities as collateral in an amount equal to or exceeding 100% of the current fair value of the loaned securities. The collateral is marked-to-market daily by State Street Bank and Trust Company ("State Street"), the securities lending agent, to ensure that a minimum of 100% collateral coverage is maintained.

Based on pre-established guidelines, the securities lending agent invests any cash collateral that is received in an affiliated money market portfolio and repurchase agreements. Securities lending income is generated from the earnings on the invested collateral and borrowing fees, less any rebates owed to the borrowers and compensation to the lending agent, and is recorded as "Income from Securities Loaned — Net" in the Fund's Statement of Operations. Risks in securities lending transactions are that a borrower may not provide additional collateral when required or return the securities when due, and that the value of the short-term investments will be less

than the amount of cash collateral plus any rebate that is required to be returned to the borrower.

The Fund has the right under the securities lending agreement to recover the securities from the borrower on demand.

The following table presents financial instruments that are subject to enforceable netting arrangements as of September 30, 2020:

Gross Amounts Not Offset in the Statement of Assets and Liabilities
Gross Asset Amounts Presented in the Statement of Assets and Liabilities (000)			Financial Instrument (000)		Collateral Received (000)			Net Amount (not less than $0) (000)
$	6,455	(e)	$	—	$	(6,455	)(f)(g)	$	0

(e) Represents market value of loaned securities at year end.

(f) The Fund received cash collateral of approximately $5,536,000, which was subsequently invested in Morgan Stanley Institutional Liquidity Funds as reported in the Portfolio of Investments. In addition, the Fund received non-cash collateral of approximately $1,058,000 in the form of U.S. Government obligations, which the Fund cannot sell or repledge, and accordingly are not reflected in the Portfolio of Investments.

(g) The actual collateral received is greater than the amount shown here due to overcollateralization.

FASB ASC 860, "Transfers & Servicing: Repurchase-to-Maturity Transactions, Repurchase Financings, and Disclosures", is intended to provide increased transparency about the types of collateral pledged in securities lending transactions and other similar transactions that are accounted for as secured borrowing.

The following table displays a breakdown of transactions accounted for as secured borrowings, the gross obligations by class of collateral pledged and the remaining contractual maturity of those transactions as of September 30, 2020:

Remaining Contractual Maturity of the Agreements
	Overnight and Continuous (000)		<30 days (000)		Between 30 & 90 days (000)		>90 days (000)		Total (000)
Securities Lending Transactions
Corporate Bonds	$	4,747	$	—	$	—	$	—	$	4,747
Sovereign		789		—		—		—		789
Total	$	5,536	$	—	$	—	$	—	$	5,536
Total Borrowings	$	5,536	$	—	$	—	$	—	$	5,536
Gross amount of recognized liabilities for securities lending transactions									$	5,536

37

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

6.  When-Issued/Delayed Delivery Securities: The Fund purchases and sells when-issued and delayed delivery securities. Securities purchased on a when-issued or delayed delivery basis are purchased for delivery beyond the normal settlement date at a stated price and yield, and no income accrues to the Fund on such securities prior to delivery date. Payment and delivery for when-issued and delayed delivery securities can take place a month or more after the date of the transaction. When the Fund enters into a purchase transaction on a when-issued or delayed delivery basis, securities are available for collateral in an amount at least equal in value to the Fund's commitments to purchase such securities. Purchasing securities on a when-issued or delayed delivery basis may involve a risk that the market price at the time of delivery may be lower than the agreed upon purchase price, in which case there could be an unrealized loss at the time of delivery. Purchasing investments on a when-issued or delayed delivery basis may be considered a form of leverage which may increase the impact that gains (losses) may have on the Fund.

7.  Indemnifications: The Trust enters into contracts that contain a variety of indemnifications. The Trust's maximum exposure under these arrangements is unknown. However, the Trust has not had prior claims or losses pursuant to these contracts and expects the risk of loss to be remote.

8.  Dividends and Distributions to Shareholders: Dividends and distributions to shareholders are recorded on the ex-dividend date. Dividends from net investment income, if any, are declared and paid monthly. Net realized capital gains, if any, are distributed at least annually.

9.  Security Transactions, Income and Expenses: Security transactions are accounted for on the trade date (date the order to buy or sell is executed). Realized gains and losses on the sale of investment securities are determined on the specific identified cost method. Dividend income and other distributions are recorded on the ex-dividend date (except for certain foreign dividends which may be recorded as soon as the Fund is informed of such dividends) net of applicable withholding taxes. Interest income is recognized on the accrual basis except where collection is in doubt. Discounts are accreted and premiums are amortized over the life of the respective securities.

Most expenses of the Trust can be directly attributed to a particular Fund. Expenses which cannot be directly attributed are apportioned among the Funds based upon relative net assets or other appropriate methods. Income, expenses (other than class specific expenses — distribution and shareholder services, transfer agency and sub transfer agency fees) and realized and unrealized gains or losses are allocated to each class of shares based upon their relative net assets.

B. Advisory Fees: The Adviser, a wholly-owned subsidiary of Morgan Stanley, provides the Fund with advisory services under the terms of an Investment Advisory Agreement, paid quarterly, at the annual rate based on the average daily net assets as follows:

First $1 billion			Over $1 billion
	0.375	%		0.300	%

For the year ended September 30, 2020, the advisory fee rate (net of waivers/rebate) was equivalent to an annual effective rate of 0.19% of the Fund's average daily net assets.

The Adviser has agreed to reduce its advisory fee and/or reimburse the Fund so that total annual Fund operating expenses, excluding certain investment related expenses, taxes, interest and other extraordinary expenses (including litigation), will not exceed 0.42% for Class I shares, 0.77% for Class A shares, 1.02% for Class L shares, 1.52% for Class C shares and 0.37% for Class IS shares. The fee waivers and/or expense reimbursements will continue for at least one year from the date of the Fund's prospectus or until such time as the Trustees act to discontinue all or a portion of such waivers and/or reimbursements when they deem such action is appropriate. For the year ended September 30, 2020, approximately $1,289,000 of advisory fees were waived and approximately $329,000 of other expenses were reimbursed by the Adviser pursuant to this arrangement.

C. Administration Fees: The Adviser also serves as Administrator to the Trust and provides administrative services pursuant to an Administration Agreement for an annual fee, accrued daily and paid monthly, of 0.08% of the Fund's average daily net assets. Under a Sub-Administration Agreement between the Administrator and State Street, State Street provides certain administrative services to the Trust. For such services, the Administrator pays State Street a portion of the fee the Administrator receives from the Fund.

38

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

D. Distribution and Shareholder Services Fees: Morgan Stanley Distribution, Inc. ("MSDI" or the "Distributor"), a wholly-owned subsidiary of the Adviser, and an indirect subsidiary of Morgan Stanley, serves as the Trust's Distributor of Fund shares pursuant to a Distribution Agreement. The Trust has adopted a Shareholder Services Plan with respect to Class A shares pursuant to Rule 12b-1 under the Act. Under the Shareholder Services Plan, the Fund pays the Distributor a shareholder services fee, accrued daily and paid monthly, at an annual rate of 0.25% of the Fund's average daily net assets attributable to Class A shares.

The Trust has adopted a Distribution and Shareholder Services Plan with respect to Class L shares pursuant to Rule 12b-1 under the Act. Under the Distribution and Shareholder Services Plan, the Fund pays the Distributor a distribution fee, accrued daily and paid monthly, at an annual rate of 0.25% and a shareholder services fee, accrued daily and paid monthly, at an annual rate of 0.25% of the Fund's average daily net assets attributable to Class L shares.

The Trust has adopted a Distribution and Shareholder Services Plan with respect to Class C shares pursuant to Rule 12b-1 under the Act. Under the Distribution and Shareholder Services Plan, the Fund pays the Distributor a distribution fee, accrued daily and paid monthly, at an annual rate of 0.75% and a shareholder services fee, accrued daily and paid monthly, at an annual rate of 0.25% of the Fund's average daily net assets attributable to Class C shares.

The distribution and shareholder services fees are used to support the expenses associated with servicing and maintaining accounts. The Distributor may compensate other parties for providing shareholder support services to investors who purchase Class A, Class L and Class C shares.

E. Dividend Disbursing and Transfer Agent: The Trust's dividend disbursing and transfer agent is DST Asset Manager Solutions, Inc. ("DST"). Pursuant to a Transfer Agency Agreement, the Trust pays DST a fee based on the number of classes, accounts and transactions relating to the Funds of the Trust.

F. Custodian Fees: State Street (the "Custodian") also serves as Custodian for the Trust in accordance with a Custodian Agreement. The Custodian holds cash, securities and other assets of the Trust as required by the Act. Custody fees are payable monthly based on assets held in custody, investment purchases and sales activity and account maintenance fees, plus reimbursement for certain out-of-pocket expenses.

G. Security Transactions and Transactions with Affiliates: For the year ended September 30, 2020, purchases and sales of investment securities for the Fund, other than long-term U.S. Government securities and short-term investments were approximately $653,794,000 and $372,705,000, respectively. For the year ended September 30, 2020, purchases and sales of long-term U.S. Government securities were approximately $1,840,548,000 and $1,809,093,000, respectively.

The Fund invests in the Institutional Class of the Morgan Stanley Institutional Liquidity Funds — Government Portfolio (the "Liquidity Funds"), an open-end management investment company managed by the Adviser, both directly and as a portion of the securities held as collateral on loaned securities. Advisory fees paid by the Fund are reduced by an amount equal to its pro-rata share of the advisory and administration fees paid by the Fund due to its investment in the Liquidity Funds. For the year ended September 30, 2020, advisory fees paid were reduced by approximately $153,000 relating to the Fund's investment in the Liquidity Funds.

A summary of the Fund's transactions in shares of affiliated investments during the year ended September 30, 2020 is as follows:

Affiliated Investment Company	Value September 30, 2019 (000)		Purchases at Cost (000)		Proceeds from Sales (000)		Dividend Income (000)
Liquidity Funds	$	57,949	$	604,747	$	502,689	$	560

Affiliated Investment Company (cont'd)	Realized Gain (Loss) (000)		Change in Unrealized Appreciation (Depreciation) (000)		Value September 30, 2020 (000)
Liquidity Funds	$	—	$	—	$	160,007

The Fund is permitted to purchase and sell securities ("cross-trade") from and to other Morgan Stanley funds as well as other funds and client accounts for which the Adviser or an affiliate of the Adviser serves as investment adviser, pursuant to procedures approved by the Trustees in compliance with Rule 17a-7 under the Act (the "Rule"). Each cross-trade is executed at the current market price in compliance with provisions of the Rule. For the year ended September 30, 2020, the Fund did not engage in any cross-trade transactions.

The Fund has an unfunded Deferred Compensation Plan (the "Compensation Plan"), which allows each independent Trustee to defer payment of all, or a portion, of the fees he or she receives for serving on the Board of Trustees. Each eligible Trustee generally may elect to have the deferred amounts credited with a return equal to the total return on one or more of

39

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

the Morgan Stanley funds that are offered as investment options under the Compensation Plan. Appreciation/depreciation and distributions received from these investments are recorded with an offsetting increase/decrease in the deferred compensation obligation and do not affect the NAV of the Fund.

H. Federal Income Taxes: It is the Fund's intention to continue to qualify as a regulated investment company and distribute all of its taxable and tax-exempt income. Accordingly, no provision for federal income taxes is required in the financial statements.

The Fund may be subject to taxes imposed by countries in which it invests. Such taxes are generally based on income and/or capital gains earned or repatriated. Taxes are accrued based on net investment income, net realized gains and net unrealized appreciation as such income and/or gains are earned. Taxes may also be based on transactions in foreign currency and are accrued based on the value of investments denominated in such currency.

FASB ASC 740-10, "Income Taxes — Overall", sets forth a minimum threshold for financial statement recognition of the benefit of a tax position taken or expected to be taken in a tax return. Management has concluded there are no significant uncertain tax positions that would require recognition in the financial statements. If applicable, the Fund recognizes interest accrued related to unrecognized tax benefits in "Interest Expense" and penalties in "Other Expenses" in the Statement of Operations. The Fund files tax returns with the U.S. Internal Revenue Service, New York and various states. Generally, each of the tax years in the four-year period ended September 30, 2020 remains subject to examination by taxing authorities.

The tax character of distributions paid may differ from the character of distributions shown for GAAP purposes due to short-term capital gains being treated as ordinary income for tax purposes. The tax character of distributions paid during fiscal years 2020 and 2019 was as follows:

2020 Distributions Paid From:				2019 Distributions Paid From:
Ordinary Income (000)		Long-Term Capital Gain (000)		Ordinary Income (000)		Long-Term Capital Gain (000)
$	21,516	$	2,668	$	14,473	$	—

The amount and character of income and gains to be distributed are determined in accordance with income tax regulations

which may differ from GAAP. These book/tax differences are either considered temporary or permanent in nature.

Temporary differences are attributable to differing book and tax treatments for the timing of the recognition of gains (losses) on certain investment transactions and the timing of the deductibility of certain expenses.

The Fund had no permanent differences causing reclassifications among the components of net assets for the year ended September 30, 2020.

At September 30, 2020, the components of distributable earnings for the Fund on a tax basis were as follows:

Undistributed Ordinary Income (000)		Undistributed Long-Term Capital Gain (000)
$	25,539	$	2,687

I. Credit Facility: The Trust and other Morgan Stanley funds participated in a $300,000,000 committed, unsecured revolving line of credit facility (the "Facility") with State Street. This Facility is to be used for temporary emergency purposes or funding of shareholder redemption requests. The interest rate on borrowings is based on the federal funds rate or 1 month LIBOR rate plus a spread. The Facility also has a commitment fee of 0.25% per annum based on the unused portion of the Facility. During the year ended September 30, 2020, the Fund did not have any borrowings under the Facility.

J. Other: At September 30, 2020, the Fund had record owners of 10% or greater. Investment activities of these shareholders could have a material impact on the Fund. The aggregate percentage of such owners was 46.4%.

K. Market Risk: Certain impacts to public health conditions particular to the coronavirus (COVID-19) outbreak could impact the operations and financial performance of certain of the Fund's investments. The extent of the impact to the financial performance of the Fund's investments will depend on future developments, including (i) the duration and spread of the outbreak, (ii) the restrictions and advisories, (iii) the effects on the financial markets, and (iv) the effects on the economy overall, all of which are highly uncertain and cannot be predicted. If the financial performance of the Fund's investments is impacted because of these factors for an extended period, the Fund's investment results may be adversely affected.

40

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

L. LIBOR Risk: The Fund's investments, payment obligations and financing terms may be based on floating rates, such as London Interbank Offer Rate ("LIBOR"), Euro Interbank Offered Rate and other similar types of reference rates (each, a "Reference Rate"). These Reference Rates are generally intended to represent the rate at which contributing banks may obtain short-term borrowings from each other within certain financial markets. On July 27, 2017, the Chief Executive of the UK Financial Conduct Authority ("FCA"), which regulates LIBOR, announced that the FCA will no longer persuade nor require banks to submit rates for the calculation of LIBOR and certain other Reference Rates after 2021. Such announcement indicates that the continuation of LIBOR and other Reference Rates on the current basis cannot and will not be guaranteed after the end of 2021. This announcement and any additional regulatory or market changes may have an adverse impact on the Fund or its investments.

In advance of 2022, regulators and market participants are currently engaged in identifying successor Reference Rates ("Alternative Reference Rates"). Additionally, prior to the end of 2021, it is expected that market participants will focus on the transition mechanisms by which the Reference Rates in existing contracts or instruments may be amended, whether through marketwide protocols, fallback contractual provisions, bespoke negotiations or amendments or otherwise. Nonetheless, the termination of certain Reference Rates presents risks to the Fund. At this time, it is not possible to completely identify or predict the effect of any such changes, any establishment of Alternative Reference Rates or any other reforms to Reference Rates that may be enacted in the UK or elsewhere. The elimination of a Reference Rate or any other changes or reforms to the determination or supervision of Reference Rates could have an adverse impact on the market for or value of any securities or payments linked to those Reference Rates and other financial obligations held by the Fund or on its overall financial condition or results of operations.

41

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Report of Independent Registered Public Accounting Firm

To the Shareholders and Board of Trustees of
Morgan Stanley Institutional Fund Trust —
Core Plus Fixed Income Portfolio

Opinion on the Financial Statements

We have audited the accompanying statement of assets and liabilities of Core Plus Fixed Income Portfolio (the "Fund") (one of the funds constituting Morgan Stanley Institutional Fund Trust (the "Trust")), including the portfolio of investments, as of September 30, 2020, and the related statement of operations for the year then ended, the statements of changes in net assets for each of the two years in the period then ended, the financial highlights for each of the five years in the period then ended and the related notes (collectively referred to as the "financial statements"). In our opinion, the financial statements present fairly, in all material respects, the financial position of the Fund (one of the funds constituting Morgan Stanley Institutional Fund Trust) at September 30, 2020, the results of its operations for the year then ended, the changes in its net assets for each of the two years in the period then ended and its financial highlights for each of the five years in the period then ended, in conformity with U.S. generally accepted accounting principles.

Basis for Opinion

These financial statements are the responsibility of the Trust's management. Our responsibility is to express an opinion on the Fund's financial statements based on our audits. We are a public accounting firm registered with the Public Company Accounting Oversight Board (United States) ("PCAOB") and are required to be independent with respect to the Trust in accordance with the U.S. federal securities law and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB.

We conducted our audits in accordance with the standards of the PCAOB. Those standards require that we plan and perform the audit to obtain reasonable assurance about whether the financial statements are free of material misstatement, whether due to error or fraud. The Trust is not required to have, nor were we engaged to perform, an audit of the Trust's internal control over financial reporting. As part of our audits we are required to obtain an understanding of internal control over financial reporting but not for the purpose of expressing an opinion on the effectiveness of the Trust's internal control over financial reporting. Accordingly, we express no such opinion.

Our audits included performing procedures to assess the risks of material misstatement of the financial statements, whether due to error or fraud, and performing procedures that respond to those risks. Such procedures included examining, on a test basis, evidence regarding the amounts and disclosures in the financial statements. Our procedures included confirmation of securities owned as of September 30, 2020 by correspondence with the custodian and brokers or by other appropriate auditing procedures where replies from brokers were not received. Our audits also included evaluating the accounting principles used and significant estimates made by management, as well as evaluating the overall presentation of the financial statements. We believe that our audits provide a reasonable basis for our opinion.

We have served as the auditor of one or more Morgan Stanley investment companies since 2000.
Boston, Massachusetts
November 24, 2020

42

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Advisory Agreement Approval (unaudited)

Nature, Extent and Quality of Services

The Board reviewed and considered the nature and extent of the investment advisory services provided by the Adviser under the advisory agreement, including portfolio management, investment research and equity and fixed income securities trading. The Board also reviewed and considered the nature and extent of the non-advisory, administrative services provided by the Administrator under the administration agreement, including accounting, operations, clerical, bookkeeping, compliance, business management and planning, legal services and the provision of supplies, office space and utilities at the Adviser's expense. The Board also considered the Adviser's investment in personnel and infrastructure that benefits the Fund. (The Adviser and Administrator together are referred to as the "Adviser" and the advisory and administration agreements together are referred to as the "Management Agreement.") The Board also considered that the Adviser serves a variety of other investment advisory clients and has experience overseeing service providers. The Board also compared the nature of the services provided by the Adviser with similar services provided by non-affiliated advisers as prepared by Broadridge Financial Solutions, Inc. ("Broadridge").

The Board reviewed and considered the qualifications of the portfolio managers, the senior administrative managers and other key personnel of the Adviser who provide the advisory and administrative services to the Fund. The Board determined that the Adviser's portfolio managers and key personnel are well qualified by education and/or training and experience to perform the services in an efficient and professional manner. The Board concluded that the nature and extent of the advisory and administrative services provided were necessary and appropriate for the conduct of the business and investment activities of the Fund and supported its decision to approve the Management Agreement.

Performance, Fees and Expenses of the Fund

The Board reviewed the performance, fees and expenses of the Fund compared to its peers, as prepared by Broadridge, and to appropriate benchmarks where applicable. The Board discussed with the Adviser the performance goals and the actual results achieved in managing the Fund. When considering a fund's performance, the Board and the Adviser place emphasis on trends and longer-term returns (focusing on one-year, three-year and five-year performance, as of December 31, 2019, or since inception, as applicable). When a fund underperforms its benchmark and/or its peer group average, the Board and the Adviser discuss the causes of such underperformance and, where necessary, they discuss specific changes to investment strategy or investment personnel. The Board noted that the Fund's performance was better than its peer group average for the one-, three- and five-year periods. The Board discussed with the Adviser the level of the advisory and administration fees (together, the "management fee") for this Fund relative to comparable funds and/or other accounts advised by the Adviser and/or compared to its peers as prepared by Broadridge. In addition to the management fee, the Board also reviewed the Fund's total expense ratio. The Board noted that the Fund's contractual management fee was higher than but close to its peer group averages and actual management fee and total expense ratio were lower than its peer group averages. After discussion, the Board concluded that the Fund's performance, management fee and total expense ratio were competitive with its peer group averages.

Economies of Scale

The Board considered the size and growth prospects of the Fund and how that relates to the Fund's total expense ratio and particularly the Fund's management fee rate, which includes a breakpoint. In conjunction with its review of the Adviser's profitability, the Board discussed with the Adviser how a change in assets can affect the efficiency or effectiveness of managing the Fund and whether the management fee level is appropriate relative to current and projected asset levels and/or whether the management fee structure reflects economies of scale as asset levels change. The Board has determined that its review of the actual and/or potential economies of scale of the Fund supports its decision to approve the Management Agreement.

Profitability of the Adviser and Affiliates

The Board considered information concerning the costs incurred and profits realized by the Adviser and its affiliates during the last year from their relationship with the Fund and during the last two years from their relationship with the Morgan Stanley Fund Complex and reviewed with the Adviser the cost allocation methodology used to determine the profitability of the Adviser and affiliates. The Board has determined that its review of the analysis of the Adviser's expenses and profitability supports its decision to approve the Management Agreement.

43

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Advisory Agreement Approval (unaudited) (cont'd)

Other Benefits of the Relationship

The Board considered other direct and indirect benefits to the Adviser and/or its affiliates derived from their relationship with the Fund and other funds advised by the Adviser. These benefits may include, among other things, fees for trading, distribution and/or shareholder servicing and for transaction processing and reporting platforms used by securities lending agents, and research received by the Adviser generated from commission dollars spent on funds' portfolio trading. The Board reviewed with the Adviser these arrangements and the reasonableness of the Adviser's costs relative to the services performed. The Board has determined that its review of the other benefits received by the Adviser or its affiliates supports its decision to approve the Management Agreement.

Resources of the Adviser and Historical Relationship Between the Fund and the Adviser

The Board considered whether the Adviser is financially sound and has the resources necessary to perform its obligations under the Management Agreement. The Board also reviewed and considered the historical relationship between the Fund and the Adviser, including the organizational structure of the Adviser, the policies and procedures formulated and adopted by the Adviser for managing the Fund's operations and the Board's confidence in the competence and integrity of the senior managers and key personnel of the Adviser. The Board concluded that the Adviser has the financial resources necessary to fulfill its obligations under the Management Agreement and that it is beneficial for the Fund to continue its relationship with the Adviser.

Other Factors and Current Trends

The Board considered the controls and procedures adopted and implemented by the Adviser and monitored by the Fund's Chief Compliance Officer and concluded that the conduct of business by the Adviser indicates a good faith effort on its part to adhere to high ethical standards in the conduct of the Fund's business.

As part of the Board's review, the Board received information from management on the impact of COVID-19 on the firm generally and the Adviser and the Fund in particular including, among other information, the pandemic's current and expected impact on the Fund's performance and operations.

General Conclusion

After considering and weighing all of the above factors, with various written materials and verbal information presented by the Adviser, the Board concluded that it would be in the best interest of the Fund and its shareholders to approve renewal of the Management Agreement for another year. In reaching this conclusion the Board did not give particular weight to any single piece of information or factor referenced above. The Board considered these factors and information over the course of the year and in numerous meetings, some of which were in executive session with only the independent Board members and their counsel present. It is possible that individual Board members may have weighed these factors, and the information presented, differently in reaching their individual decisions to approve the Management Agreement.

44

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Liquidity Risk Management Program (unaudited)

In compliance with Rule 22e-4 under the Investment Company Act of 1940, as amended (the "Liquidity Rule"), the Fund has adopted and implemented a liquidity risk management program (the "Program"), which is reasonably designed to assess and manage the risk that the Fund could not meet requests to redeem shares issued by the Fund without significant dilution of remaining investors' interests in the Fund (i.e., liquidity risk). The Fund's Board of Trustees (the "Board") previously approved the designation of the Liquidity Risk Subcommittee (the "LRS") as Program administrator. The LRS is comprised of representatives from various divisions within Morgan Stanley Investment Management.

At a meeting held on April 22-23, 2020, the Board reviewed a written report prepared by the LRS that addressed the Program's operation and assessed its adequacy, and effectiveness of implementation for the period from December 1, 2018, through December 31, 2019, as required under the Liquidity Rule. The report concluded that the Program operated effectively and was adequately and effectively implemented in all material aspects, and that the relevant controls and safeguards were appropriately designed to enable the LRS to administer the Program in compliance with the Liquidity Rule.

In accordance with the Program, the LRS assessed each Fund's liquidity risk no less frequently than annually taking into consideration certain factors, as applicable, such as (i) investment strategy and liquidity of portfolio investments, (ii) short-term and long-term cash flow projections and (iii) holdings of cash and cash equivalents and borrowing arrangements and other funding sources. Certain factors are considered under both normal and reasonably foreseeable stressed conditions.

Each Fund portfolio investment is classified into one of four liquidity categories, which classification is assessed at least monthly by the LRS. The classification is based on a determination of the number of days it is reasonably expected to take to convert the investment into cash, or sell or dispose of the investment, in current market conditions without significantly changing the market value of the investment. Liquidity classification determinations take into account various market, trading and investment-specific considerations, as well as market depth, and in some cases utilize third-party vendor data.

The Liquidity Rule limits a fund's investments in illiquid investments to 15% of its net assets and requires funds that do not primarily hold assets that are highly liquid investments to determine and maintain a minimum percentage of the fund's net assets to be invested in highly liquid investments (highly liquid investment minimum or "HLIM"). The LRS believes that the Program includes provisions reasonably designed to review, monitor and comply with the 15% limit on illiquid investments and for determining, periodically reviewing and complying with the HLIM requirement, as applicable.

There can be no assurance that the Program will achieve its objectives under all circumstances in the future. Please refer to the Fund's prospectus for more information regarding the Fund's exposure to liquidity risk and other risks to which it may be subject.

45

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Federal Tax Notice (unaudited)

For federal income tax purposes, the following information is furnished with respect to the distributions paid by the Fund during its taxable year ended September 30, 2020.

The Fund designated and paid approximately $2,668,000 as a long-term capital gain distribution.

For federal income tax purposes, the following information is furnished with respect to the Fund's earnings for its taxable year ended September 30, 2020. The Fund designated up to a maximum of approximately $6,442,000 as qualifying as interest-related dividends.

In January, the Fund provides tax information to shareholders for the preceding calendar year.

46

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Privacy Notice (unaudited)  April 2019

FACTS	WHAT DOES MSIM DO WITH YOUR PERSONAL INFORMATION?
Why?	Financial companies choose how they share your personal information. Federal law gives consumers the right to limit some but not all sharing. Federal law also requires us to tell you how we collect, share, and protect your personal information. Please read this notice carefully to understand what we do.
What?	The types of personal information we collect and share depend on the product or service you have with us. This information can include: n Social Security number and income n investment experience and risk tolerance n checking account number and wire transfer instructions
How?	All financial companies need to share customers' personal information to run their everyday business. In the section below, we list the reasons financial companies can share their customers' personal information; the reasons MSIM chooses to share; and whether you can limit this sharing.

Reasons we can share your personal information	Does MSIM share?	Can you limit this sharing?
For our everyday business purposes — such as to process your transactions, maintain your account(s), respond to court orders and legal investigations, or report to credit bureaus	Yes	No
For our marketing purposes — to offer our products and services to you	Yes	No
For joint marketing with other financial companies	No	We don't share
For our affiliates' everyday business purposes — information about your transactions and experiences	Yes	No
For our affiliates' everyday business purposes — information about your creditworthiness	No	We don't share
For our affiliates to market to you	No	We don't share
For non-affiliates to market to you	No	We don't share

Questions?Call toll-free (844) 312-6327 or email: imprivacyinquiries@morganstanley.com

47

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Privacy Notice (unaudited) (cont'd)  April 2019

Who we are

Who is providing this notice? Morgan Stanley Investment Management, Inc. and its affiliated registered investment advisers, registered broker-dealers, and registered and unregistered funds ("MSIM")

What we do

How does MSIM protect my personal information?	To protect your personal information from unauthorized access and use, we use security measures that comply with federal law. These measures include computer safeguards and secured files and buildings. We have policies governing the proper handling of customer information by personnel and requiring third parties that provide support to adhere to appropriate security standards with respect to such information.
How does MSIM collect my personal information?	We collect your personal information, for example, when you n open an account or make deposits or withdrawals from your account n buy securities from us or make a wire transfer n give us your contact information We also collect your personal information from others, such as credit bureaus, affiliates, or other companies.
Why can't I limit all sharing?	Federal law gives you the right to limit only n sharing for affiliates' everyday business purposes — information about your creditworthiness n affiliates from using your information to market to you n sharing for non-affiliates to market to you State laws and individual companies may give you additional rights to limit sharing. See below for more on your rights under state law.

Definitions

Affiliates	Companies related by common ownership or control. They can be financial and non-financial companies. n Our affilies include companies with a Morgan Stanley name and financial companies such as Morgan Stanley Smith Barney LLC and Morgan Stanley & Co.
Non-affiliates	Companies not related by common ownership or control. They can be financial and non-financial companies. n MSIM does not share with non-affiliates so they can market to you.
Joint marketing	A formal agreement between non-affiliated financial companies that together market financial products or services to you. n MSIM doesn't jointly market

Other Important Information

Vermont: Except as permitted by law, we will not share personal information we collect about Vermont residents with Non-affiliates unless you provide us with your written consent to share such information.

California: Except as permitted by law, we will not share personal information we collect about California residents with Non-affiliates and we will limit sharing such personal information with our Affiliates to comply with California privacy laws that apply to us.

48

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited)

Independent Trustees:

Name, Address and Birth Year of Independent Trustee	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years and Other Relevant Professional Experience	Number of Funds in Fund Complex Overseen by Independent Trustee**	Other Directorships Held by Independent Trustee***
Frank L. Bowman c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1944	Trustee	Since August 2006	President, Strategic Decisions, LLC (consulting) (since February 2009); Director or Trustee of various Morgan Stanley Funds (since August 2006); Chairperson of the Compliance and Insurance Committee (since October 2015); formerly, Chairperson of the Insurance Sub-Committee of the Compliance and Insurance Committee (2007-2015); served as President and Chief Executive Officer of the Nuclear Energy Institute (policy organization) (February 2005-November 2008); retired as Admiral, U.S. Navy after serving over 38 years on active duty including 8 years as Director of the Naval Nuclear Propulsion Program in the Department of the Navy and the U.S. Department of Energy (1996-2004); served as Chief of Naval Personnel (July 1994-September 1996) and on the Joint Staff as Director of Political Military Affairs (June 1992-July 1994); knighted as Honorary Knight Commander of the Most Excellent Order of the British Empire; awarded the Officier de l'Orde National du Mérite by the French Government; elected to the National Academy of Engineering (2009).	86	Director of Naval and Nuclear Technologies LLP; Director Emeritus of the Armed Services YMCA; Member of the National Security Advisory Council of the Center for U.S. Global Engagement and a member of the CNA Military Advisory Board; Trustee of Fairhaven United Methodist Church; Member of the Board of Advisors of the Dolphin Scholarship Foundation; Director of other various non-profit organizations; Formerly, Director of BP p.l.c. (November 2010-May 2019).
Kathleen A. Dennis c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1953	Trustee	Since August 2006	President, Cedarwood Associates (mutual fund and investment management consulting) (since July 2006); Chairperson of the Liquidity and Alternatives Sub-Committee of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 2006); formerly, Senior Managing Director of Victory Capital Management (1993-2006).	86	Director of various non-profit organizations.
Nancy C. Everett c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1955	Trustee	Since January 2015	Chief Executive Officer, Virginia Commonwealth University Investment Company (since November 2015); Owner, OBIR, LLC (institutional investment management consulting) (since June 2014); formerly, Managing Director, BlackRock, Inc. (February 2011-December 2013); and Chief Executive Officer, General Motors Asset Management (a/k/a Promark Global Advisors, Inc.) (June 2005-May 2010).	87	Formerly, Member of Virginia Commonwealth University School of Business Foundation (2005-2016); Member of Virginia Commonwealth University Board of Visitors (2013-2015); Member of Committee on Directors for Emerging Markets Growth Fund, Inc. (2007-2010); Chairperson of Performance Equity Management, LLC (2006-2010); and Chairperson, GMAM Absolute Return Strategies Fund, LLC (2006-2010).

49

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Address and Birth Year of Independent Trustee	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years and Other Relevant Professional Experience	Number of Funds in Fund Complex Overseen by Independent Trustee**	Other Directorships Held by Independent Trustee***
Jakki L. Haussler c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1957	Trustee	Since January 2015	Chairman, Opus Capital Group (since January 1996); formerly, Chief Executive Officer, Opus Capital Group (1996-2019); Director, Capvest Venture Fund, LP (May 2000-December 2011); Partner, Adena Ventures, LP (July 1999-December 2010); Director, The Victory Funds (February 2005-July 2008).	87	Director of Service Corporation International and Member, Audit Committee and Investment Committee; Director of Cincinnati Bell Inc. and Member, Audit Committee and Governance and Nominating Committee; Director of Northern Kentucky University Foundation and Member, Investment Committee; Member of Chase College of Law Transactional Law Practice Center Board of Advisors; Director of Chase College of Law Board of Visitors; formerly, Member, University of Cincinnati Foundation Investment Committee; Member, Miami University Board of Visitors (2008-2011); Trustee of Victory Funds (2005-2008) and Chairman, Investment Committee (2007-2008); Member, Service Provider Committee (2005-2008) and Director of Best Transport (2006-2019).
Dr. Manuel H. Johnson c/o Johnson Smick International, Inc. 220 I Street, NE — Suite 200 Washington, D.C. 20002 Birth Year 1949	Trustee	Since July 1991	Senior Partner, Johnson Smick International, Inc. (consulting firm); Chairperson of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since July 1991); Co-Chairman and a founder of the Group of Seven Council (G7C) (international economic commission); formerly, Chairperson of the Audit Committee (July 1991-September 2006), Vice Chairman of the Board of Governors of the Federal Reserve System and Assistant Secretary of the U.S. Treasury.	86	Director of NVR, Inc. (home construction).
Joseph J. Kearns c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1942	Trustee	Since August 1994	Senior Adviser, Kearns & Associates LLC (investment consulting); Chairperson of the Audit Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 1994); Director, Rubicorn Investments (since February 2019); formerly, Deputy Chairperson of the Audit Committee (July 2003-September 2006) and Chairperson of the Audit Committee of various Morgan Stanley Funds (since August 1994); CFO of the J. Paul Getty Trust (1982-1999).	87	Prior to August 10, 2016, Director of Electro Rent Corporation (equipment leasing); Prior to December 31, 2013, Director of The Ford Family Foundation.

50

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Address and Birth Year of Independent Trustee	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years and Other Relevant Professional Experience	Number of Funds in Fund Complex Overseen by Independent Trustee**	Other Directorships Held by Independent Trustee***
Michael F. Klein c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1958	Trustee	Since August 2006	Managing Director, Aetos Alternatives Management, LP (since March 2000); Co-President, Aetos Alternatives Management, LP (since January 2004) and Co-Chief Executive Officer of Aetos Alternatives Management, LP (since August 2013); Chairperson of the Fixed Income Sub-Committee of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 2006); formerly, Managing Director, Morgan Stanley & Co. Inc. and Morgan Stanley Dean Witter Investment Management and President, various Morgan Stanley Funds (June 1998-March 2000); Principal, Morgan Stanley & Co. Inc. and Morgan Stanley Dean Witter Investment Management (August 1997-December 1999).	86	Director of certain investment funds managed or sponsored by Aetos Alternatives Management, LP; Director of Sanitized AG and Sanitized Marketing AG (specialty chemicals).
Patricia Maleski c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1960	Trustee	Since January 2017	Managing Director, JPMorgan Asset Management (2004-2016); Oversight and Control Head of Fiduciary and Conflicts of Interest Program (2015-2016); Chief Control Officer-Global Asset Management (2013-2015); President, JPMorgan Funds (2010-2013); Chief Administrative Officer (2004-2013); various other positions including Treasurer and Board Liaison (since 2001).	87	None.
W. Allen Reed c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1947	Chair of the Board and Trustee	Chair of the Boards since August 2020 and Trustee since August 2006	Chair of the Boards of various Morgan Stanley Funds (since August 2020); Chairperson of the Governance Committee; Chairperson of the Equity Sub-Committee of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 2006); formerly, Vice Chair of the Boards of various Morgan Stanley Funds (January 2020-August 2020); President and Chief Executive Officer of General Motors Asset Management; Chairman and Chief Executive Officer of the GM Trust Bank and Corporate Vice President of General Motors Corporation (August 1994-December 2005).	86	Formerly, Director of Legg Mason, Inc. (2006-2019); and Director of the Auburn University Foundation (2010-2015).

*  This is the earliest date the Trustee began serving the Morgan Stanley Funds. Each Trustee serves an indefinite term, until his or her successor is elected.

**  The Fund Complex includes (as of December 31, 2019) all open-end and closed-end funds (including all of their portfolios) advised by Morgan Stanley Investment Management Inc. (the "Adviser") and any funds that have an adviser that is an affiliated person of the Adviser (including, but not limited to, Morgan Stanley AIP GP LP).

***  This includes any directorships at public companies and registered investment companies held by the Trustee at any time during the past five years.

51

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited) (cont'd)

Executive Officers:

Name, Address and Birth Year of Executive Officer	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years
John H. Gernon 522 Fifth Avenue New York, NY 10036 Birth Year 1963	President and Principal Executive Officer	Since September 2013	President and Principal Executive Officer of the Equity and Fixed Income Funds and the Morgan Stanley AIP Funds (since September 2013) and the Liquidity Funds and various money market funds (since May 2014) in the Fund Complex; Managing Director of the Adviser; Head of Public Markets Product Development (since 2006).
Timothy J. Knierim 522 Fifth Avenue New York, NY 10036 Birth Year 1959	Chief Compliance Officer	Since December 2016	Managing Director of the Adviser and various entities affiliated with the Adviser; Chief Compliance Officer of various Morgan Stanley Funds and the Adviser (since December 2016) and Chief Compliance Officer of Morgan Stanley AIP GP LP (since 2014). Formerly, Managing Director and Deputy Chief Compliance Officer of the Adviser (2014-2016); and formerly, Chief Compliance Officer of Prudential Investment Management, Inc. (2007-2014).
Francis J. Smith 522 Fifth Avenue New York, NY 10036 Birth Year 1965	Treasurer and Principal Financial Officer	Treasurer since July 2003 and Principal Financial Officer since September 2002	Managing Director of the Adviser and various entities affiliated with the Adviser; Treasurer (since July 2003) and Principal Financial Officer of various Morgan Stanley Funds (since September 2002).
Mary E. Mullin 522 Fifth Avenue New York, NY 10036 Birth Year 1967	Secretary	Since June 1999	Managing Director of the Adviser; Secretary of various Morgan Stanley Funds (since June 1999).
Michael J. Key 522 Fifth Avenue New York, NY 10036 Birth Year 1979	Vice President	Since June 2017	Vice President of the Equity and Fixed Income Funds, Liquidity Funds, various money market funds and the Morgan Stanley AIP Funds in the Fund Complex (since June 2017); Executive Director of the Adviser; Head of Product Development for Equity and Fixed Income Funds (since August 2013).

*  This is the earliest date the officer began serving the Morgan Stanley Funds. Each officer serves a one-year term, until his or her successor is elected and qualifies.

52

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Adviser and Administrator

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

Distributor

Morgan Stanley Distribution, Inc.
522 Fifth Avenue
New York, New York 10036

Dividend Disbursing and Transfer Agent

DST Asset Manager Solutions, Inc.
2000 Crown Colony Drive
Quincy, Massachusetts 02169

Custodian

State Street Bank and Trust Company
One Lincoln Street
Boston, Massachusetts 02111

Legal Counsel

Dechert LLP
1095 Avenue of the Americas
New York, New York 10036

Counsel to the Independent Trustees

Perkins Coie LLP
1155 Avenue of the Americas,
22nd Floor
New York, New York 10036

Independent Registered Public Accounting Firm

Ernst & Young LLP
200 Clarendon Street
Boston, Massachusetts 02116

Reporting to Shareholders

Each Morgan Stanley fund provides a complete schedule of portfolio holdings in its Semi-Annual and the Annual Reports within 60 days of the end of the fund's second and fourth fiscal quarters. The Semi-Annual and Annual Reports are filed electronically with the Securities and Exchange Commission ("SEC") on Form N-CSRS and Form N-CSR, respectively. Morgan Stanley also delivers the Semi-Annual and Annual Reports to fund shareholders and makes these reports available on its public website, www.morganstanley.com/im/shareholderreports. Each Morgan Stanley non-money market fund also files a complete schedule of portfolio holdings with the SEC for the fund's first and third fiscal quarters as an attachment to Form N-PORT. Morgan Stanley does not deliver the reports for the first and third fiscal quarters to shareholders, nor are the reports posted to the Morgan Stanley public website. However, the holdings for each money market fund are posted to the Morgan Stanley public website. You may obtain the Form N-PORT filings (as well as the Form N-CSR and N-CSRS filings) by accessing the SEC's website, www.sec.gov. You can also request copies of these materials, upon payment of a duplicating fee, by electronic request at the SEC's email address (publicinfo@sec.gov).

Proxy Voting Policies and Procedures and Proxy Voting Record

You may obtain a copy of the Trust's Proxy Voting Policy and Procedures and information regarding how the Trust voted proxies relating to portfolio securities during the most recent twelve-month period ended June 30, without charge, upon request, by calling toll free 1 (800) 548-7786 or by visiting our website at www.morganstanley.com/im/shareholderreports. This information is also available on the SEC's website at www.sec.gov.

This report is authorized for distribution only when preceded or accompanied by a prospectus or summary prospectus of the applicable Fund of Morgan Stanley Institutional Fund Trust, which describes in detail the Fund's investment policies, risks, fees and expenses. Please read the prospectus carefully before you invest or send money. For additional information, including information regarding the investments comprising the Fund, please visit our website at www.morganstanley.com/im/shareholderreports or call toll free 1 (800) 548-7786.

53

Printed in U.S.A.
This Report has been prepared for shareholders and may be distributed to others only if preceded or accompanied by a current prospectus.

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

© 2020 Morgan Stanley. Morgan Stanley Distribution, Inc.

IFTCPFIANN
3298732 EXP 11.30.21

INVESTMENT MANAGEMENT

Morgan Stanley Institutional Fund Trust

Corporate Bond Portfolio

Annual Report

September 30, 2020

Beginning on January 1, 2021, as permitted by regulations adopted by the Securities and Exchange Commission ("SEC"), paper copies of the Fund's Annual and Semi-Annual Reports to Shareholders ("Shareholder Reports") will no longer be sent by mail, unless you specifically request paper copies of the Shareholder Reports from the Fund or from your financial intermediary, such as a broker-dealer or a bank. Instead, the Shareholder Reports will be made available on the Fund's website, https://www.morganstanley.com/im/shareholderreports and you will be notified by mail each time a Shareholder Report is posted and provided with a website link to access the Shareholder Report. If you already elected to receive Shareholder Reports electronically, you will not be affected by this change and you need not take any action. You may elect to receive Shareholder Reports and other communications from the Fund electronically anytime by contacting your financial intermediary or, if you are a direct investor, please follow the instructions on the envelope.

Beginning on January 1, 2019, you may elect to receive all future Shareholder Reports in paper free of charge. If you invest through a financial intermediary, you can contact your financial intermediary to request that you continue to receive paper copies of your Shareholder Reports. If you invest directly with the Fund, please follow the instructions on the envelope to let the Fund know you wish to continue receiving paper copies of your Shareholder Reports. Your election to receive Shareholder Reports in paper will apply to all funds held in your account if you invest through your financial intermediary or all funds held with the fund complex if you invest directly with a fund.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Table of Contents

Shareholders' Letter	2
Expense Example	3
Investment Overview	4
Portfolio of Investments	7
Statement of Assets and Liabilities	15
Statement of Operations	17
Statements of Changes in Net Assets	18
Financial Highlights	19
Notes to Financial Statements	23
Report of Independent Registered Public Accounting Firm	34
Investment Advisory Agreement Approval	35
Liquidity Risk Management Program	37
Privacy Notice	38
Trustee and Officer Information	40

This report is authorized for distribution only when preceded or accompanied by a prospectus or summary prospectus of the applicable Fund of the Morgan Stanley Institutional Fund Trust. To receive a prospectus and/or statement of additional information ("SAI"), which contains more complete information such as investment objectives, charges, expenses, policies for voting proxies, risk considerations and describes in detail each of the Fund's investment policies to the prospective investor, please call toll free 1 (800) 548-7786. Please read the prospectuses carefully before you invest or send money.

Additionally, you can access information about the Fund, including performance, characteristics and investment team commentary, through Morgan Stanley Investment Management's website: www.morganstanley.com/im/shareholderreports.

Market forecasts provided in this report may not necessarily come to pass. There is no guarantee that any sectors mentioned will continue to perform as discussed herein or that securities in such sectors will be held by the Fund in the future. There is no assurance that a fund will achieve its investment objective. Funds are subject to market risk, which is the possibility that market values of securities owned by the Fund will decline and, therefore, the value of the Fund's shares may be less than what you paid for them. Accordingly, you can lose money investing in this Fund. Please see the prospectus for more complete information on investment risks.

1

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Shareholders' Letter (unaudited)

Dear Shareholders,

We are pleased to provide this Annual Report, in which you will learn how your investment in Corporate Bond Portfolio (the "Fund") performed during the latest twelve-month period.

Morgan Stanley Investment Management is a client-centric, investor-led organization. Our global presence, intellectual capital, and breadth of products and services enable us to partner with investors to meet the evolving challenges of today's financial markets. We aim to deliver superior investment service and to empower our clients to make the informed decisions that help them reach their investment goals.

As always, we thank you for selecting Morgan Stanley Investment Management, and look forward to working with you in the months and years ahead.

Sincerely,

John H. Gernon
President and Principal Executive Officer

October 2020

2

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Expense Example (unaudited)

Corporate Bond Portfolio

As a shareholder of the Fund, you may incur two types of costs: (1) transactional costs, including sales charge (loads) on purchase payments; and (2) ongoing costs, which may include advisory fees, administration fees, distribution and shareholder services fees; and other Fund expenses. This example is intended to help you understand your ongoing costs (in dollars) of investing in the Fund and to compare these costs with the ongoing costs of investing in other mutual funds.

This example is based on an investment of $1,000 invested at the beginning of the six-month period ended September 30, 2020 and held for the entire six-month period.

Actual Expenses

The table below provides information about actual account values and actual expenses. You may use the information in this table, together with the amount you invested, to estimate the expenses that you paid over the period. Simply divide your account value by $1,000 (for example, an $8,600 account value divided by $1,000 = 8.6), then multiply the result by the number in the table under the heading entitled "Actual Expenses Paid During Period" to estimate the expenses you paid on your account during this period.

Hypothetical Example for Comparison Purposes

The table below provides information about hypothetical account values and hypothetical expenses based on the Fund's actual expense ratio and an assumed rate of return of 5% per year before expenses, which is not the Fund's actual return. The hypothetical account values and expenses may not be used to estimate the actual ending account balance or expenses you paid for the period. You may use this information to compare the ongoing costs of investing in the Fund and other funds. To do so, compare this 5% hypothetical example with the 5% hypothetical examples that appear in the shareholder reports of the other funds.

Please note that the expenses shown in the table are meant to highlight your ongoing costs only and do not reflect any transactional costs, such as sales charges (loads, if applicable). Therefore, the information for each class in the table is useful in comparing ongoing costs only, and will not help you determine the relative total costs of owning different funds. In addition, if these transactional costs were included, your costs would have been higher.

	Beginning Account Value 4/1/20		Actual Ending Account Value 9/30/20		Hypothetical Ending Account Value		Actual Expenses Paid During Period*		Hypothetical Expenses Paid During Period*		Net Expense Ratio During Period**
Corporate Bond Portfolio Class I	$	1,000.00	$	1,120.40	$	1,021.50	$	3.71	$	3.54		0.70	%
Corporate Bond Portfolio Class A		1,000.00		1,117.60		1,019.85		5.45		5.20		1.03
Corporate Bond Portfolio Class L		1,000.00		1,116.50		1,017.95		7.46		7.11		1.41
Corporate Bond Portfolio Class C		1,000.00		1,114.20		1,016.00		9.51		9.07		1.80

*  Expenses are calculated using each Fund Class' annualized net expense ratio (as disclosed), multiplied by the average account value over the period and multiplied by 183/366 (to reflect the most recent one-half year period).

**  Annualized.

3

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Overview (unaudited)

Corporate Bond Portfolio

The Fund seeks above-average total return over a market cycle of three to five years.

Performance

For the fiscal year ended September 30, 2020, the Fund's Class I shares had a total return based on net asset value and reinvestment of distributions per share of 8.19%, net of fees. The Fund's Class I shares outperformed against the Fund's benchmark, the Bloomberg Barclays U.S. Corporate Index (the "Index"), which returned 7.90%.

Factors Affecting Performance

•  The final quarter of 2019 provided a remarkable ending to a remarkable year. The world's issues seemed to vanish as financial markets rallied. Credit markets enjoyed meaningful tightening in their spreads. The Index spread fell 22 basis points (bps) to end December 2019 at 93 bps over government bonds, its tightest level of the year (and 60 bps tighter than where they started the year).ⁱ Risk was rewarded, as lower quality and longer maturity bonds performed the best. The key drivers of tighter spreads were (1) a reported agreement on a U.S.-China "phase one" trade deal, (2) a victory for the Tories in the U.K. election reducing Brexit uncertainty, (3) macroeconomic data continuing a stabilization trend, (4) minimal negative corporate news, and (5) low supply in a period of strong demand.

•  The virus-induced economic shutdown and the decline in oil prices hit credit markets with a double whammy in the first quarter of 2020, leading to historically poor performance of corporate bonds. The Index spread widened by 179 bps to end March 2020 at 272 bps over government bonds.ⁱ The stressed liquidity conditions in the market could be seen in the flattening of the spread curve, as shorter maturity corporate bonds, which are often viewed as a cash surrogate, widened the most. The 1- to 3-year portion of the Index widened by 218 bps, versus "only" 138 bps for long-maturity corporate bonds in the first quarter of 2020.ⁱ BBB-rated bonds underperformed their higher-rated counterparts, as worries about ratings downgrades to high yield credit swept the market.

•  Markets enjoyed a historic bounce back in the second quarter of 2020, after a volatile COVID-19

and lockdown-driven first quarter. Equities rallied and credit spreads moved tighter. Spreads on the Index ended the second quarter at 150 bps over government bonds, after gapping as wide as 373 bps on March 23, 2020, during the peak of the crisis.ⁱ Spreads were only 57 bps wider in the year-to-date through June 30, 2020.ⁱ During the second quarter, financials outperformed non-financials, and a continued theme of beta compression helped BBB-rated bonds outperform A-rated credits. Additionally, given the Federal Reserve's (Fed) support to stabilize the credit markets amid coronavirus-related impacts, the short end of the yield curve outperformed the long end.

•  The market continued to recover during the third quarter of 2020, though it ran out of steam in September amid a pickup in virus cases and uncertainty surrounding the prospect of another stimulus package ahead of the U.S. election. The Index tightened 14 bps in the third quarter to end at 136 bps over government bonds.ⁱ The Index produced total returns of 1.54% during the third quarter, bringing year-to-date returns to 6.64%. Lower quality outperformed as BBB-rated bonds tightened 21 bps.ⁱ Third quarter 2020 investment grade bond issuance was $371 billion, up 17% year-over-year.ⁱⁱ This increase was primarily driven by the strong issuance activity observed in August and September 2020, which offset the slowdown in July. Third quarter 2020 supply was down sharply from $692 billion in the second quarter of 2020 and $480 billion in the first quarter of 2020.ⁱⁱ Nevertheless, year-to-date through September 2020, investment grade bond issuance reached $1.54 trillion, which is $290 billion above the prior full-year record high of $1.25 trillion.ⁱⁱ We would note that the first wave of supply specifically addressed liquidity needs, while the second wave of supply was driven by issuers taking advantage of improving market conditions and historically low rates.

•  In terms of positioning, we have not actively changed the portfolio's key risk positions. As of September 30, 2020, the Fund is positioned to be modestly underweight credit risk as a whole. The portfolio's largest overweight remains financials, which contributed positively to returns over the period. The Fund's underweight positioning to the consumer non-cyclical and capital goods sectors also

ⁱ  Source: Bloomberg Barclays.

ⁱⁱ  Source: JP Morgan. Data as September 30, 2020.

4

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020 (unaudited)

Investment Overview (cont'd)

Corporate Bond Portfolio

contributed positively to returns. Overall positioning in energy and communications detracted from returns, as did exposure to airlines.

•  Small allocations to off-index sectors also contributed significantly over the period. The Fund's allocation to high yield bonds contributed positively to returns as several fallen angels rallied over the period. Exposure to convertible bonds was also particularly beneficial as convertible bond performance has been a leader among fixed income categories, largely due to the rise in equity volatility. As volatility rises, embedded equity options become more valuable.

•  While we had reduced BBB-rated industrial exposure back in 2019 on valuation grounds, recently we have been selectively increasing our exposure to this space at attractive valuations. In addition, while high-level exposures may not look very different, we were quite active at a more idiosyncratic security level. We were very active in the new issue market, especially in the second quarter of 2020 when supply was especially elevated and new issue concessions remained higher.

Management Strategies

•  We remain cautiously optimistic on investment grade corporate debt on the back of continued global monetary and fiscal policy accommodation. On the other hand, our relatively constructive view is tempered by less compelling valuations, increased volatility due to the upcoming U.S. presidential election, and some setbacks on the fight against the pandemic, as evidenced in increasing case counts in Europe and stricter lockdown measures imposed in several countries. Our base case reflects the consensus view that the coronavirus is transitory and monetary policy is credit risk friendly, likely driving spreads tighter in the medium term and offering investors yield advantages but limited capital gain.

5

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020 (unaudited)

Investment Overview (cont'd)

Corporate Bond Portfolio

*  Minimum Investment

In accordance with SEC regulations, the Fund's performance shown assumes that all recurring fees (including management fees) were deducted and all dividends and distributions were reinvested. The performance of Class A, Class L and Class C shares will vary from the performance of Class I shares based upon their different inception dates and will be negatively impacted by additional fees assessed to those classes.

Performance Compared to the Bloomberg Barclays U.S. Corporate Index⁽¹⁾ and the Lipper Corporate Debt Funds BBB-Rated Index⁽²⁾

	Period Ended September 30, 2020 Total Returns(3)
				Average Annual
	One Year			Five Years			Ten Years			Since Inception(8)
Fund — Class I Shares w/o sales charges(4)		8.19	%		7.77	%		6.12	%		6.51	%
Fund — Class A Shares w/o sales charges(5)		7.88			7.43			5.84			4.86
Fund — Class A Shares with maximum 3.25% sales charges(5)		4.38			6.72			5.49			4.67
Fund — Class L Shares w/o sales charges(6)		7.47			7.05			5.47			5.27
Fund — Class C Shares w/o sales charges(7)		7.09			6.60			—			5.40
Fund — Class C Shares with maximum 1.00% deferred sales charges(7)		6.09			6.60			—			5.40
Bloomberg Barclays U.S. Corporate Index		7.90			5.98			5.14			6.89
Lipper Corporate Debt Funds BBB-Rated Index		6.95			5.83			5.12			6.49

Performance data quoted represents past performance, which is no guarantee of future results, and current performance may be lower or higher than the figures shown. Performance assumes that all dividends and distributions, if any, were reinvested. For the most recent month-end performance figures, please visit www.morganstanley.com/im/shareholderreports. Investment returns and principal value will fluctuate so that Fund shares, when redeemed, may be worth more or less than their original cost. Total returns do not reflect the deduction of taxes that a shareholder would pay on Fund distributions or the redemption of Fund shares. Performance of share classes will vary due to differences in sales charges and expenses.

⁽¹⁾  The Bloomberg Barclays U.S. Corporate Index is a broad-based benchmark that measures the investment grade, U.S. dollar-denominated, fixed rate, taxable corporate bond market. It includes USD-denominated securities publicly issued by U.S. and non-U.S. industrial, utility and financial issuers that meet specified maturity, liquidity and quality requirements.The Index is unmanaged and its returns do not include any sales charges or fees. Such costs would lower performance. It is not possible to invest directly in an index.

⁽²⁾  The Lipper Corporate Debt Funds BBB-Rated Index is an equally weighted performance index of the largest qualifying funds (based on net assets) in the Lipper Corporate Debt Funds BBB-Rated Funds classification. The Index, which is adjusted for capital gains distributions and income dividends, is unmanaged and should not be considered an investment. There are currently 30 funds represented in this Index. As of the date of this report, the Fund was in the Lipper Corporate Debt Funds BBB-Rated Funds classification.

⁽³⁾  Total returns for the Fund reflect expenses waived and/or reimbursed, if applicable, by the Adviser and Distributor. Without such waivers and/or reimbursements, total returns would have been lower.

⁽⁴⁾  Commenced operations on August 31, 1990.

⁽⁵⁾  Commenced offering on May 20, 2002.

⁽⁶⁾  Commenced offering on June 16, 2008.

⁽⁷⁾  Commenced offering on April 30, 2015.

⁽⁸⁾  For comparative purposes, average annual since inception returns listed for the Indexes refer to the inception date of Class I of the Fund, not the inception of the Indexes.

6

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments

Corporate Bond Portfolio

	Face Amount (000)		Value (000)
Fixed Income Securities (96.1%)
Corporate Bonds (96.1%)
Communications (0.2%)
Vodafone Group PLC
5.13%, 6/19/59	$	250	$	321
Energy (0.4%)
Equinor ASA
3.70%, 4/6/50		300		346
Midwest Connector Capital Co. LLC
3.63%, 4/1/22 (a)(b)		375		378
				724
Finance (35.3%)
Aflac, Inc.,
3.60%, 4/1/30		350		412
Air Lease Corp.,
2.50%, 3/1/21		650		654
3.75%, 6/1/26		600		611
Alexandria Real Estate Equities, Inc.,
1.88%, 2/1/33		325		319
American Express Co.,
4.20%, 11/6/25		550		638
American International Group, Inc.,
4.25%, 3/15/29		300		352
Aon Corp.,
2.20%, 11/15/22		300		311
2.80%, 5/15/30		500		543
Arch Capital Group Ltd.,
3.64%, 6/30/50		300		324
Avolon Holdings Funding Ltd.,
2.88%, 2/15/25 (a)		550		505
Banco de Credito del Peru
2.70%, 1/11/25 (a)		325		339
Banco Santander Chile
2.70%, 1/10/25 (a)		425		449
Bank of America Corp.,
2.59%, 4/29/31		400		427
2.68%, 6/19/41		1,436		1,474
3.19%, 7/23/30		125		138
4.24%, 4/24/38		341		416
4.25%, 10/22/26		475		551
7.75%, 5/14/38		175		290
Barclays PLC
2.85%, 5/7/26		1,225		1,275
BBVA USA,
2.50%, 8/27/24		325		339
3.50%, 6/11/21		975		993
Belrose Funding Trust
2.33%, 8/15/30 (a)		1,200		1,189
Berkshire Hathaway Finance Corp.,
1.85%, 3/12/30		475		498
BNP Paribas SA
4.40%, 8/14/28 (a)		850		998

	Face Amount (000)		Value (000)
BPCE SA
5.15%, 7/21/24 (a)	$	1,025	$	1,150
Brookfield Finance LLC
3.45%, 4/15/50		250		245
Brookfield Finance, Inc.,
3.90%, 1/25/28		325		362
4.00%, 4/1/24		300		331
4.85%, 3/29/29		150		179
Brown & Brown, Inc.,
2.38%, 3/15/31		650		655
4.20%, 9/15/24		325		359
Capital One Financial Corp.,
3.30%, 10/30/24		1,625		1,763
3.75%, 3/9/27		125		139
Chubb INA Holdings, Inc.,
1.38%, 9/15/30		1,050		1,040
Citigroup, Inc.,
1.68%, 5/15/24		375		384
2.57%, 6/3/31		225		236
2.67%, 1/29/31		1,674		1,766
2.98%, 11/5/30		428		463
4.45%, 9/29/27		1,025		1,190
CNO Financial Group, Inc.,
5.25%, 5/30/29		260		301
Commerzbank AG
8.13%, 9/19/23 (a)		550		625
Credit Agricole SA
4.13%, 1/10/27 (a)		250		287
Credit Suisse Group AG
2.59%, 9/11/25 (a)		675		705
Crown Castle International Corp.,
4.15%, 7/1/50		200		229
3.30%, 7/1/30		575		630
CubeSmart
2.00%, 2/15/31		775		766
CyrusOne LP/CyrusOne Finance Corp.,
2.90%, 11/15/24		100		106
Danske Bank A/S,
3.00%, 9/20/22 (a)		425		433
5.00%, 1/12/23 (a)		200		210
Deutsche Bank AG,
3.15%, 1/22/21		625		629
3.70%, 5/30/24		100		105
Discover Financial Services
3.95%, 11/6/24		625		688
Duke Realty LP
1.75%, 7/1/30		775		773
Equitable Financial Life Global Funding
1.40%, 7/7/25 - 8/27/27 (a)		1,000		1,016
ERP Operating LP
4.63%, 12/15/21		600		624
Federal Realty Investment Trust
3.63%, 8/1/46		225		225

The accompanying notes are an integral part of the financial statements.
7

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Corporate Bond Portfolio

	Face Amount (000)		Value (000)
Finance (cont'd)
Five Corners Funding Trust II
2.85%, 5/15/30 (a)	$	750	$	807
GE Capital International Funding Co., Unlimited Co.,
4.42%, 11/15/35		486		514
General Electric Co.,
MTN
5.88%, 1/14/38		400		469
Global Atlantic Fin Co.,
4.40%, 10/15/29 (a)		925		965
GLP Capital LP/GLP Financing II, Inc.,
4.00%, 1/15/30		350		363
Goldman Sachs Group, Inc. (The),
3.69%, 6/5/28		250		281
MTN
4.80%, 7/8/44		275		361
6.75%, 10/1/37		950		1,383
Grupo Aval Ltd.,
4.38%, 2/4/30 (a)		625		604
Hartford Financial Services Group, Inc. (The),
2.80%, 8/19/29		775		843
High Street Funding Trust I
4.11%, 2/15/28 (a)		850		980
HSBC Holdings PLC
2.63%, 11/7/25		625		652
4.29%, 9/12/26		750		838
4.38%, 11/23/26		625		690
ING Groep N.V.,
4.63%, 1/6/26 (a)		1,000		1,175
Intercontinental Exchange, Inc.,
1.85%, 9/15/32		950		949
Itau Unibanco Holding SA
2.90%, 1/24/23 (a)		850		861
JPMorgan Chase & Co.,
2.52%, 4/22/31		175		187
2.96%, 5/13/31		1,200		1,291
3.70%, 5/6/30		2,450		2,816
JPMorgan Chase Bank NA
0.00%, 8/7/22		200		254
Kemper Corp.,
2.40%, 9/30/30		500		496
Kilroy Realty LP
2.50%, 11/15/32		200		195
3.05%, 2/15/30		150		157
Kimco Realty Corp.,
3.70%, 10/1/49		275		271
LeasePlan Corp.,
2.88%, 10/24/24 (a)		675		697
Lloyds Banking Group PLC
3.57%, 11/7/28		425		466
Macquarie Bank Ltd.,
3.62%, 6/3/30 (a)		800		852

	Face Amount (000)		Value (000)
Marsh & McLennan Cos., Inc.,
2.25%, 11/15/30	$	875	$	917
MDC GMTN BV
4.50%, 11/7/28 (a)		425		510
MetLife, Inc.,
5.88%, 2/6/41		350		511
Metropolitan Life Global Funding I
2.95%, 4/9/30 (a)		350		393
National Australia Bank Ltd.,
2.33%, 8/21/30 (a)(b)		850		843
National Securities Clearing Corp.,
1.50%, 4/23/25 (a)		450		464
Nationwide Building Society
4.30%, 3/8/29 (a)		275		311
4.36%, 8/1/24 (a)		500		543
Oversea-Chinese Banking Corp. Ltd.,
1.83%, 9/10/30 (a)(b)		390		390
Pine Street Trust I
4.57%, 2/15/29 (a)		375		436
PNC Financial Services Group, Inc. (The),
2.20%, 11/1/24		675		715
Progressive Corp. (The),
3.20%, 3/26/30		450		516
4.00%, 3/1/29		75		91
Prologis LP
1.25%, 10/15/30		1,050		1,029
Quicken Loans LLC/ Quicken Loans Co-Issuer, Inc.,
3.88%, 3/1/31 (a)		290		287
Royal Bank of Scotland Group PLC
3.88%, 9/12/23		1,075		1,154
Santander UK Group Holdings PLC
4.80%, 11/15/24		575		634
Santander UK PLC
5.00%, 11/7/23 (a)		369		404
Shinhan Bank Co., Ltd.,
4.00%, 4/23/29 (a)		600		676
Shinhan Financial Group Co. Ltd.,
1.35%, 1/10/26 (a)		460		461
Societe Generale SA
2.63%, 1/22/25 (a)		625		645
SVB Financial Group
3.13%, 6/5/30		400		447
Synchrony Financial
4.25%, 8/15/24		175		190
Syngenta Finance N.V.,
4.89%, 4/24/25 (a)		300		325
TD Ameritrade Holding Corp.,
3.30%, 4/1/27		325		365
Transurban Finance Co. Pty Ltd.,
2.45%, 3/16/31 (a)		800		817
UnitedHealth Group, Inc.,
3.70%, 8/15/49		700		839

The accompanying notes are an integral part of the financial statements.
8

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Corporate Bond Portfolio

	Face Amount (000)		Value (000)
Finance (cont'd)
Wells Fargo & Co.,
2.41%, 10/30/25	$	225	$	236
2.57%, 2/11/31		475		500
2.88%, 10/30/30		525		565
3.07%, 4/30/41		525		552
				69,842
Industrials (51.5%)
Abbott Laboratories
1.15%, 1/30/28		1,125		1,135
AbbVie, Inc.,
3.20%, 11/21/29 (a)		1,525		1,687
4.25%, 11/21/49 (a)		700		835
Activision Blizzard, Inc.,
2.50%, 9/15/50		425		398
Adobe, Inc.,
2.30%, 2/1/30		525		566
Air Products and Chemicals, Inc.,
2.80%, 5/15/50		425		456
Airbus SE
0.00%, 6/14/21	EUR	300		350
Akamai Technologies, Inc.,
0.38%, 9/1/27	$	344		400
Aker BP ASA
4.75%, 6/15/24 (a)		575		591
Alaska Airlines 2020-1 Class A Pass Through Trust
4.80%, 2/15/29 (a)		325		342
Alphabet, Inc.,
1.10%, 8/15/30		475		474
Altria Group, Inc.,
3.88%, 9/16/46		175		180
Amazon.com, Inc.,
2.50%, 6/3/50		325		334
4.25%, 8/22/57		500		685
American Airlines Pass-Through Trust,
Series AA
3.15%, 8/15/33		676		641
Amgen, Inc.,
2.45%, 2/21/30		675		717
2.77%, 9/1/53 (a)		200		193
4.66%, 6/15/51		25		33
Anheuser-Busch Cos. LLC/Anheuser-Busch InBev Worldwide, Inc.,
3.65%, 2/1/26		425		477
Anheuser-Busch InBev Worldwide, Inc.,
4.60%, 4/15/48		150		179
5.55%, 1/23/49		1,100		1,484
Anthem, Inc.,
2.38%, 1/15/25		275		293
3.65%, 12/1/27		450		513
Apple, Inc.,
2.95%, 9/11/49		1,100		1,209

	Face Amount (000)		Value (000)
APT Pipelines Ltd.,
4.20%, 3/23/25 (a)	$	300	$	331
AstraZeneca PLC
1.38%, 8/6/30		525		512
AT&T, Inc.,
2.25%, 2/1/32		1,225		1,230
3.30%, 2/1/52		225		215
3.50%, 9/15/53 (a)		445		432
3.55%, 9/15/55 (a)		177		172
3.65%, 9/15/59 (a)		778		768
4.50%, 3/9/48		22		25
Automatic Data Processing, Inc.,
1.25%, 9/1/30		850		841
Aviation Capital Group LLC
4.38%, 1/30/24 (a)		475		473
BAT Capital Corp.,
3.56%, 8/15/27		675		730
3.73%, 9/25/40		525		529
BEST BUY Co., Inc.,
1.95%, 10/1/30		625		622
Boeing Co. (The),
3.25%, 2/1/35		150		141
3.90%, 5/1/49		225		208
3.95%, 8/1/59		175		159
5.15%, 5/1/30		500		563
Booking Holdings, Inc.,
0.90%, 9/15/21		225		240
Boston Scientific Corp.,
2.65%, 6/1/30		975		1,037
BP Capital Markets PLC
4.38%, 12/31/99 (c)		500		522
4.88%, 12/31/99 (c)		525		563
Braskem Netherlands Finance BV
4.50%, 1/31/30 (a)		340		318
Bristol-Myers Squibb Co.,
3.40%, 7/26/29		575		671
4.25%, 10/26/49		75		99
4.35%, 11/15/47		125		166
Broadcom, Inc.,
4.15%, 11/15/30		650		732
Burlington Northern Santa Fe LLC
4.40%, 3/15/42		75		94
4.55%, 9/1/44		610		798
Campbell Soup Co.
3.13%, 4/24/50		450		457
Canadian National Railway Co.,
2.45%, 5/1/50		375		374
Canadian Natural Resources Ltd.,
2.95%, 1/15/23		650		676
Caterpillar, Inc.,
3.25%, 9/19/49		225		253

The accompanying notes are an integral part of the financial statements.
9

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Corporate Bond Portfolio

	Face Amount (000)		Value (000)
Industrials (cont'd)
Charter Communications Operating LLC/ Charter Communications Operating Capital
2.80%, 4/1/31	$	375	$	391
5.75%, 4/1/48		275		344
Chevron Corp.,
2.24%, 5/11/30		750		798
Cigna Corp.,
2.40%, 3/15/30		375		390
3.05%, 10/15/27		150		167
3.88%, 10/15/47		125		139
4.80%, 7/15/46		125		157
Cimarex Energy Co.,
3.90%, 5/15/27		475		479
4.38%, 3/15/29 (b)		425		440
Clorox Co. (The),
1.80%, 5/15/30		525		542
Coca-Cola Femsa SAB de CV
2.75%, 1/22/30		600		640
Comcast Corp.,
1.95%, 1/15/31		575		593
2.80%, 1/15/51		375		382
3.75%, 4/1/40		175		206
4.05%, 11/1/52		725		895
4.25%, 1/15/33		375		467
Conagra Brands, Inc.,
4.85%, 11/1/28		375		459
Concho Resources, Inc.,
4.85%, 8/15/48		250		275
Cummins, Inc.,
2.60%, 9/1/50		375		369
CVS Health Corp.,
1.75%, 8/21/30		275		269
3.75%, 4/1/30		787		900
5.05%, 3/25/48		200		256
5.13%, 7/20/45		75		95
Daimler Finance North America LLC
2.70%, 6/14/24 (a)		325		344
Dell International LLC/EMC Corp.,
4.90%, 10/1/26 (a)		750		849
Delta Air Lines, Inc.,
Series AA
3.20%, 10/25/25		450		450
3.63%, 3/15/22		475		467
Diamond Sports Group LLC/Diamond Sports Finance Co.,
6.63%, 8/15/27 (a)		200		104
Diamondback Energy, Inc.,
3.25%, 12/1/26		700		703
Dollar General Corp.,
4.13%, 4/3/50		325		387
DP World PLC
5.63%, 9/25/48 (a)		500		572

	Face Amount (000)		Value (000)
DuPont de Nemours, Inc.,
5.32%, 11/15/38	$	225	$	286
Embraer Netherlands Finance BV
5.40%, 2/1/27		330		314
Enbridge, Inc.
3.13%, 11/15/29		150		160
Energy Transfer Operating LP
5.00%, 5/15/50		175		163
Enterprise Products Operating LLC
3.95%, 1/31/60		125		124
4.20%, 1/31/50		575		613
4.80%, 2/1/49		250		290
Equinix, Inc.,
1.55%, 3/15/28 (d)		600		602
Exxon Mobil Corp.,
3.10%, 8/16/49		200		205
Fiserv, Inc.,
2.65%, 6/1/30		250		270
Ford Motor Credit Co., LLC
4.39%, 1/8/26		725		718
Fortune Brands Home & Security, Inc.,
4.00%, 9/21/23		475		520
Fox Corp.,
5.58%, 1/25/49		225		312
General Mills, Inc.,
2.88%, 4/15/30		925		1,017
General Motors Co.,
6.60%, 4/1/36		325		396
6.75%, 4/1/46		150		185
General Motors Financial Co., Inc.,
3.85%, 1/5/28		75		79
4.35%, 1/17/27		175		190
Georgia-Pacific LLC
2.30%, 4/30/30 (a)		675		718
Glencore Funding LLC
2.50%, 9/1/30 (a)		600		585
4.13%, 3/12/24 (a)		325		353
Global Payments, Inc.,
2.90%, 5/15/30		725		777
Grifols SA
2.25%, 11/15/27 (a)	EUR	200		234
HCA, Inc.,
5.50%, 6/15/47	$	350		435
Home Depot, Inc. (The),
2.95%, 6/15/29		300		339
3.13%, 12/15/49		75		84
3.30%, 4/15/40		200		228
3.35%, 4/15/50		200		233
Hormel Foods Corp.
1.80%, 6/11/30		400		414
Hyundai Capital America
2.38%, 2/10/23 (a)		500		514
3.00%, 2/10/27 (a)		775		803

The accompanying notes are an integral part of the financial statements.
10

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Corporate Bond Portfolio

	Face Amount (000)		Value (000)
Industrials (cont'd)
Imperial Brands Finance PLC
3.13%, 7/26/24 (a)	$	800	$	847
Industrias Penoles SAB de CV
4.75%, 8/6/50 (a)		250		259
Intel Corp.,
3.25%, 11/15/49		700		787
International Business Machines Corp.,
4.15%, 5/15/39		700		860
Inversiones CMPC SA
3.85%, 1/13/30		200		219
J2 Global, Inc.
1.75%, 11/1/26 (a)		270		240
JetBlue Pass Through Trust Series AA
2.75%, 11/15/33		494		486
John Deere Capital Corp.,
2.45%, 1/9/30		775		844
Johnson Controls International plc/ Tyco Fire & Security Finance SCA
1.75%, 9/15/30		400		403
Kimberly-Clark de Mexico SAB de CV
2.43%, 7/1/31 (a)		275		280
Kinder Morgan, Inc.,
5.20%, 3/1/48		325		382
Lam Research Corp.,
3.13%, 6/15/60		300		322
Las Vegas Sands Corp.,
3.20%, 8/8/24		925		936
Level 3 Financing, Inc.,
3.40%, 3/1/27 (a)		625		674
Lowe's Cos., Inc.,
2.50%, 4/15/26		575		624
4.50%, 4/15/30		225		280
Marathon Petroleum Corp.,
4.70%, 5/1/25		300		340
4.75%, 12/15/23		1,125		1,235
Mars, Inc.,
3.20%, 4/1/30 (a)		300		343
McDonald's Corp.,
1.45%, 9/1/25		650		671
Microsoft Corp.,
2.40%, 8/8/26		675		738
2.53%, 6/1/50		625		658
4.45%, 11/3/45		325		460
Mondelez International, Inc.,
2.75%, 4/13/30		675		736
MPLX LP
5.20%, 12/1/47		100		110
NetApp, Inc.,
1.88%, 6/22/25		1,175		1,219
Newcastle Coal Infrastructure Group Pty Ltd.,
4.40%, 9/29/27 (a)		1,125		1,121

	Face Amount (000)		Value (000)
Newmont Corp.,
2.25%, 10/1/30	$	425	$	440
5.45%, 6/9/44		225		321
NIKE, Inc.,
3.38%, 3/27/50		400		470
Nissan Motor Co. Ltd.,
3.04%, 9/15/23 (a)		650		659
NOVA Chemicals Corp.,
4.88%, 6/1/24 (a)		300		299
Nuance Communications, Inc.,
1.00%, 12/15/35		251		366
Nutrition & Biosciences, Inc.,
2.30%, 11/1/30 (a)		250		252
Nvent Finance Sarl
3.95%, 4/15/23		1,075		1,122
NVIDIA Corp.,
3.50%, 4/1/50		425		501
NXP BV/NXP Funding LLC/NXP USA, Inc.,
3.40%, 5/1/30 (a)		875		961
Occidental Petroleum Corp.,
3.50%, 8/15/29		200		154
Oracle Corp.,
3.60%, 4/1/50		125		142
3.85%, 4/1/60		275		327
4.00%, 11/15/47		475		565
Patterson-UTI Energy, Inc.,
3.95%, 2/1/28		126		98
PayPal Holdings, Inc.,
2.30%, 6/1/30		684		725
2.85%, 10/1/29		202		223
Phillips 66
2.15%, 12/15/30		275		268
POSCO
4.00%, 8/1/23 (a)		475		511
Prosus NV
3.68%, 1/21/30 (a)		200		216
Pure Storage, Inc.,
0.13%, 4/15/23		55		54
Q-Park Holding I BV
1.50%, 3/1/25 (a)	EUR	150		161
Raytheon Technologies Corp.,
4.50%, 6/1/42	$	450		570
Resorts World Las Vegas LLC/ RWLV Capital, Inc.,
4.63%, 4/16/29 (a)(b)		500		472
Rockies Express Pipeline LLC
3.60%, 5/15/25 (a)		400		393
Roper Technologies, Inc.,
1.00%, 9/15/25		600		602
Ross Stores, Inc.,
4.80%, 4/15/30		950		1,159
Royalty Pharma PLC
2.20%, 9/2/30 (a)		750		750

The accompanying notes are an integral part of the financial statements.
11

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Corporate Bond Portfolio

	Face Amount (000)		Value (000)
Industrials (cont'd)
Sabine Pass Liquefaction LLC
4.50%, 5/15/30 (a)	$	1,200	$	1,355
Saudi Arabian Oil Co.,
3.50%, 4/16/29 (a)		500		551
Shell International Finance BV
3.13%, 11/7/49		400		411
Sherwin-Williams Co. (The),
2.30%, 5/15/30		775		811
2.95%, 8/15/29		175		193
3.30%, 5/15/50		150		159
Sigma Finance Netherlands BV
4.88%, 3/27/28 (a)		200		221
Silgan Holdings, Inc.,
2.25%, 6/1/28	EUR	200		229
Smithfield Foods, Inc.,
3.00%, 10/15/30 (a)	$	75		75
5.20%, 4/1/29 (a)		775		907
Sprint Spectrum Co., LLC/Sprint Spectrum Co., II LLC/Sprint Spectrum Co., III LLC
4.74%, 9/20/29 (a)		400		434
5.15%, 9/20/29 (a)		550		649
Standard Industries, Inc.,
2.25%, 11/21/26 (a)	EUR	100		113
Sunoco Logistics Partners Operations LP
3.90%, 7/15/26	$	275		283
4.00%, 10/1/27		325		332
T-Mobile USA, Inc.,
3.88%, 4/15/30 (a)		400		454
4.50%, 4/15/50 (a)		400		481
Tencent Holdings Ltd.,
3.60%, 1/19/28 (a)		675		744
TJX Cos., Inc.,
4.50%, 4/15/50		450		583
Transcontinental Gas Pipe Line Co. LLC
3.25%, 5/15/30 (a)		450		487
Transportadora de Gas Internacional SA ESP
5.55%, 11/1/28 (a)		400		453
TSMC Global Ltd.,
0.75%, 9/28/25 (a)(b)		550		545
TWDC Enterprises 18 Corp.,
Series B
7.00%, 3/1/32		75		113
Twitter, Inc.
1.00%, 9/15/21		280		279
Union Pacific Corp.,
3.25%, 2/5/50		550		610
Upjohn, Inc.,
4.00%, 6/22/50 (a)		500		536
Verint Systems, Inc.,
1.50%, 6/1/21		225		228

	Face Amount (000)		Value (000)
Verizon Communications, Inc.,
3.88%, 2/8/29	$	650	$	771
4.33%, 9/21/28		300		364
4.67%, 3/15/55		200		278
5.01%, 4/15/49		775		1,120
Visa, Inc.,
2.70%, 4/15/40		225		244
Walmart, Inc.,
3.70%, 6/26/28		625		740
Walt Disney Co. (The),
2.75%, 9/1/49		784		768
3.60%, 1/13/51		331		374
Western Midstream Operating LP
4.10%, 2/1/25		375		358
Williams Cos., Inc. (The),
4.85%, 3/1/48		200		224
5.10%, 9/15/45		225		253
Zillow Group, Inc.,
2.00%, 12/1/21		205		398
				101,796
Utilities (8.7%)
Avangrid, Inc.,
3.80%, 6/1/29		625		724
Boston Gas Co.,
3.00%, 8/1/29 (a)		525		579
4.49%, 2/15/42 (a)		125		155
Cleveland Electric Illuminating Co. (The),
4.55%, 11/15/30 (a)		250		299
Consorcio Transmantaro SA
4.70%, 4/16/34 (a)		400		474
Consumers Energy Co.,
2.50%, 5/1/60		325		307
3.50%, 8/1/51		275		323
DTE Electric Co.,
3.95%, 3/1/49		450		569
Duke Energy Corp.,
2.45%, 6/1/30		875		925
Duke Energy Indiana LLC
Series YYY
3.25%, 10/1/49		250		280
Duke Energy Progress LLC
3.45%, 3/15/29		550		635
Enel Finance International N.V.,
6.00%, 10/7/39 (a)		200		273
Entergy Arkansas LLC
3.50%, 4/1/26		458		519
Entergy Louisiana LLC
3.05%, 6/1/31		75		86
FirstEnergy Corp.,
Series C
3.40%, 3/1/50		450		439

The accompanying notes are an integral part of the financial statements.
12

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Corporate Bond Portfolio

	Face Amount (000)		Value (000)
Utilities (cont'd)
Interstate Power and Light Co.,
2.30%, 6/1/30	$	350	$	370
3.50%, 9/30/49		175		194
Liberty Utilities Finance GP 1
2.05%, 9/15/30 (a)		875		865
Mississippi Power Co.,
3.95%, 3/30/28		575		661
NextEra Energy Capital Holdings, Inc.,
2.25%, 6/1/30		1,050		1,090
NiSource, Inc.,
1.70%, 2/15/31		500		493
2.95%, 9/1/29		400		435
Northern States Power Co.,
2.90%, 3/1/50		275		296
Oglethorpe Power Corp.,
5.05%, 10/1/48		325		385
ONEOK, Inc.,
3.10%, 3/15/30		725		699
Pacific Gas and Electric Co.,
3.15%, 1/1/26 (b)		175		180
3.30%, 8/1/40		225		208
3.50%, 8/1/50		200		181
PacifiCorp
2.70%, 9/15/30		825		908
Public Service Co. of Colorado
Series 34
3.20%, 3/1/50		275		313
Southern California Edison Co.,
4.00%, 4/1/47		250		269
Southern Co. (The),
4.40%, 7/1/46		850		1,010
Virginia Electric and Power Co.,
Series A
2.88%, 7/15/29		825		928
Series B
3.30%, 12/1/49 (b)		350		407
Xcel Energy, Inc.,
2.60%, 12/1/29		775		839
				17,318
Total Fixed Income Securities (Cost $181,198)				190,001

	Shares		Value (000)
Short-Term Investments (5.5%)
Securities held as Collateral on Loaned Securities (1.6%)
Investment Company (1.6%)
Morgan Stanley Institutional Liquidity Funds — Government Portfolio — Institutional Class (See Note G) (Cost $3,247)		3,247,060	$	3,247
Investment Company (2.9%)
Morgan Stanley Institutional Liquidity Funds — Government Portfolio — Institutional Class (See Note G) (Cost $5,785)		5,785,051		5,785
	Face Amount (000)
U.S. Treasury Security (1.0%)
U.S. Treasury Bill
0.16%, 1/28/21 (e)(f) (Cost $1,864)	$	1,865		1,864
Total Short-Term Investments (Cost $10,896)				10,896
Total Investments (101.6%) (Cost $192,094) Including $3,559 of Securities Loaned (g)(h)				200,897
Liabilities in Excess of Other Assets (–1.6%)				(3,071	)
Net Assets (100.0%)			$	197,826

(a)  144A security — Certain conditions for public sale may exist. Unless otherwise noted, these securities are deemed to be liquid.

(b)  All or a portion of this security was on loan at September 30, 2020.

(c)  Perpetual — One or more securities do not have a predetermined maturity date. Rates for these securities are fixed for a period of time, after which they revert to a floating rate. Interest rates in effect are as of September 30, 2020.

(d)  When-issued security.

(e)  Rate shown is the yield to maturity at September 30, 2020.

(f)  All or a portion of the security was pledged to cover margin requirements for futures contracts and swap agreement.

(g)  Securities are available for collateral in connection with purchase of a when-issued security, open foreign currency forward exchange contract, open futures contracts and swap agreement.

(h)  At September 30, 2020, the aggregate cost for federal income tax purposes is approximately $192,153,000. The aggregate gross unrealized appreciation is approximately $10,284,000 and the aggregate gross unrealized depreciation is approximately $1,540,000, resulting in net unrealized appreciation of approximately $8,744,000.

MTN  Medium Term Note.

The accompanying notes are an integral part of the financial statements.
13

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Corporate Bond Portfolio

Foreign Currency Forward Exchange Contract:

The Fund had the following foreign currency forward exchange contract open at September 30, 2020:

Counterparty	Contracts to Deliver (000)		In Exchange For (000)		Delivery Date	Unrealized Appreciation (000)
Citibank NA	EUR	954	$	1,137	12/1/20	$	17

Futures Contracts:

The Fund had the following futures contracts open at September 30, 2020:

	Number of Contracts		Expiration Date	Notional Amount (000)			Value (000)			Unrealized Appreciation (Depreciation) (000)
Long:
U.S. Treasury 2 yr. Note		80	Dec-20	$	16,000		$	17,677		$	8
U.S. Treasury 5 yr. Note		74	Dec-20		7,400			9,326			13
U.S. Treasury Long Bond		94	Dec-20		9,400			16,570			(137	)
U.S. Treasury Ultra Bond		13	Dec-20		1,300			2,884			2
Short:
German Euro Bund		2	Dec-20	EUR	(200	)		(409	)		(3	)
German Euro BOBL		1	Dec-20		(100	)		(158	)		(—	@)
U.S. Treasury 10 yr. Ultra Long Bond		221	Dec-20	$	(22,100	)		(35,343	)		(66	)
U.S. Treasury 10 yr. Note		17	Dec-20		(1,700	)		(2,372	)		(2	)
										$	(185	)

Credit Default Swap Agreement:

The Fund had the following credit default swap agreement open at September 30, 2020:

Swap Counterparty and Reference Obligation	Credit Rating of Reference Obligation†	Buy/Sell Protection	Pay/Receive Fixed Rate			Payment Frequency	Maturity Date	Notional Amount (000)		Value (000)			Upfront Payment (Received) (000)			Unrealized Appreciation (000)
Morgan Stanley & Co. LLC* CDX.NA.HY.33	NR	Buy		5.00	%	Quarterly	12/20/24	$	1,224	$	(65	)	$	(117	)	$	52

@    Value is less than $500.

†    Credit rating as issued by Standard & Poor's.

*    Cleared swap agreement, the broker is Morgan Stanley & Co., LLC.

NR    Not rated.

EUR    Euro

Portfolio Composition**

Classification	Percentage of Total Investments
Industrials		51.5	%
Finance		35.3
Utilities		8.8
Short-Term Investments		3.9
Other***		0.5
Total Investments		100.0	%****

**  Percentages indicated are based upon total investments (excluding Securities held as Collateral on Loaned Securities) as of September 30, 2020.

***  Industries and/or investment types representing less than 5% of total investments.

****  Does not include open long/short futures contracts with a value of approximately $84,739,000 and net unrealized depreciation of approximately $185,000. Does not include an open foreign currency forward exchange contract with total unrealized appreciation of approximately $17,000. Does not include an open swap agreement with total unrealized appreciation of approximately $52,000.

The accompanying notes are an integral part of the financial statements.
14

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Corporate Bond Portfolio

Statement of Assets and Liabilities	September 30, 2020 (000)
Assets:
Investments in Securities of Unaffiliated Issuers, at Value(1) (Cost $183,062)	$	191,865
Investment in Security of Affiliated Issuer, at Value (Cost $9,032)		9,032
Total Investments in Securities, at Value (Cost $192,094)		200,897
Foreign Currency, at Value (Cost $3)		3
Cash		4
Interest Receivable		1,544
Receivable for Investments Sold		1,438
Receivable for Fund Shares Sold		971
Unrealized Appreciation on Foreign Currency Forward Exchange Contract		17
Receivable for Variation Margin on Futures Contracts		1
Receivable from Affiliate		—	@
Receivable from Securities Lending Income		—	@
Other Assets		63
Total Assets		204,938
Liabilities:
Collateral on Securities Loaned, at Value		3,247
Payable for Investments Purchased		2,894
Payable for Fund Shares Redeemed		622
Payable for Advisory Fees		98
Payable for Professional Fees		74
Payable for Trustees' Fees and Expenses		42
Payable for Transfer Agency Fees — Class I		27
Payable for Transfer Agency Fees — Class A		1
Payable for Transfer Agency Fees — Class L		—	@
Payable for Transfer Agency Fees — Class C		1
Deferred Capital Gain Country Tax		26
Payable for Sub Transfer Agency Fees — Class I		16
Payable for Sub Transfer Agency Fees — Class A		1
Payable for Sub Transfer Agency Fees — Class L		—	@
Payable for Sub Transfer Agency Fees — Class C		—	@
Payable for Administration Fees		13
Payable for Custodian Fees		12
Payable for Shareholder Services Fees — Class A		1
Payable for Distribution and Shareholder Services Fees — Class L		1
Payable for Distribution and Shareholder Services Fees — Class C		2
Payable for Variation Margin on Swap Agreements		2
Other Liabilities		32
Total Liabilities		7,112
Net Assets	$	197,826
Net Assets Consist of:
Paid-in-Capital	$	182,545
Total Distributable Earnings		15,281
Net Assets	$	197,826

The accompanying notes are an integral part of the financial statements.
15

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Corporate Bond Portfolio

Statement of Assets and Liabilities (cont'd)	September 30, 2020 (000)
CLASS I:
Net Assets	$	182,070
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		13,497,545
Net Asset Value, Offering and Redemption Price Per Share	$	13.49
CLASS A:
Net Assets	$	10,807
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		800,252
Net Asset Value, Redemption Price Per Share	$	13.50
Maximum Sales Load		3.25	%
Maximum Sales Charge	$	0.45
Maximum Offering Price Per Share	$	13.95
CLASS L:
Net Assets	$	1,727
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		127,985
Net Asset Value, Offering and Redemption Price Per Share	$	13.49
CLASS C:
Net Assets	$	3,222
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		240,314
Net Asset Value, Offering and Redemption Price Per Share	$	13.41
(1) Including: Securities on Loan, at Value:	$	3,559

@  Amount is less than $500.

The accompanying notes are an integral part of the financial statements.
16

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Corporate Bond Portfolio

Statement of Operations	Year Ended September 30, 2020 (000)
Investment Income:
Interest from Securities of Unaffiliated Issuers (Net of $—@ of Foreign Taxes Withheld)	$	4,803
Dividends from Security of Affiliated Issuer (Note G)		24
Income from Securities Loaned — Net		6
Total Investment Income		4,833
Expenses:
Advisory Fees (Note B)		569
Professional Fees		171
Transfer Agency Fees — Class I (Note E)		116
Transfer Agency Fees — Class A (Note E)		3
Transfer Agency Fees — Class L (Note E)		2
Transfer Agency Fees — Class C (Note E)		3
Administration Fees (Note C)		121
Sub Transfer Agency Fees — Class I		97
Sub Transfer Agency Fees — Class A		8
Sub Transfer Agency Fees — Class L		1
Sub Transfer Agency Fees — Class C		2
Registration Fees		65
Shareholder Services Fees — Class A (Note D)		20
Distribution and Shareholder Services Fees — Class L (Note D)		8
Distribution and Shareholder Services Fees — Class C (Note D)		23
Custodian Fees (Note F)		44
Shareholder Reporting Fees		37
Pricing Fees		32
Trustees' Fees and Expenses		7
Other Expenses		26
Total Expenses		1,355
Reimbursement of Class Specific Expenses — Class I (Note B)		(213	)
Reimbursement of Class Specific Expenses — Class C (Note B)		(2	)
Waiver of Advisory Fees (Note B)		(9	)
Waiver of Shareholder Servicing Fees — Class A (Note D)		(8	)
Rebate from Morgan Stanley Affiliate (Note G)		(5	)
Net Expenses		1,118
Net Investment Income		3,715
Realized Gain (Loss):
Investments Sold (Net of $5 of Capital Gain Country Tax)		7,930
Foreign Currency Forward Exchange Contracts		(76	)
Foreign Currency Translation		(1	)
Futures Contracts		353
Swap Agreements		(971	)
Net Realized Gain		7,235
Change in Unrealized Appreciation (Depreciation):
Investments (Net of Decrease in Deferred Capital Gain Country Tax of $11)		193
Foreign Currency Forward Exchange Contract		17
Foreign Currency Translation		(—	@)
Futures Contracts		(21	)
Swap Agreements		546
Net Change in Unrealized Appreciation (Depreciation)		735
Net Realized Gain and Change in Unrealized Appreciation (Depreciation)		7,970
Net Increase in Net Assets Resulting from Operations	$	11,685

@  Amount is less than $500.

The accompanying notes are an integral part of the financial statements.
17

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Corporate Bond Portfolio

Statements of Changes in Net Assets	Year Ended September 30, 2020 (000)			Year Ended September 30, 2019 (000)
Increase (Decrease) in Net Assets:
Operations:
Net Investment Income	$	3,715		$	3,980
Net Realized Gain		7,235			1,004
Net Change in Unrealized Appreciation (Depreciation)		735			9,503
Net Increase in Net Assets Resulting from Operations		11,685			14,487
Dividends and Distributions to Shareholders:
Class I		(3,443	)		(4,270	)
Class A		(177	)		(176	)
Class L		(32	)		(48	)
Class C		(36	)		(77	)
Total Dividends and Distributions to Shareholders		(3,688	)		(4,571	)
Capital Share Transactions:(1)
Class I:
Subscribed		76,817			19,935
Distributions Reinvested		3,197			3,813
Redeemed		(27,783	)		(19,161	)
Class A:
Subscribed		7,693			3,735
Distributions Reinvested		176			175
Redeemed		(3,877	)		(2,440	)
Class L:
Exchanged		—			83
Distributions Reinvested		32			48
Redeemed		(67	)		(93	)
Class C:
Subscribed		2,884			1,752
Distributions Reinvested		36			77
Redeemed		(2,601	)		(1,396	)
Net Increase in Net Assets Resulting from Capital Share Transactions		56,507			6,528
Total Increase in Net Assets		64,504			16,444
Net Assets:
Beginning of Period		133,322			116,878
End of Period	$	197,826		$	133,322
(1) Capital Share Transactions:
Class I:
Shares Subscribed		5,836			1,647
Shares Issued on Distributions Reinvested		246			318
Shares Redeemed		(2,162	)		(1,607	)
Net Increase in Class I Shares Outstanding		3,920			358
Class A:
Shares Subscribed		582			303
Shares Issued on Distributions Reinvested		14			14
Shares Redeemed		(296	)		(199	)
Net Increase in Class A Shares Outstanding		300			118
Class L:
Shares Exchanged		—			8
Shares Issued on Distributions Reinvested		2			4
Shares Redeemed		(5	)		(8	)
Net Increase (Decrease) in Class L Shares Outstanding		(3	)		4
Class C:
Shares Subscribed		221			150
Shares Issued on Distributions Reinvested		3			6
Shares Redeemed		(204	)		(113	)
Net Increase in Class C Shares Outstanding		20			43

The accompanying notes are an integral part of the financial statements.
18

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Corporate Bond Portfolio

	Class I
	Year Ended September 30,
Selected Per Share Data and Ratios	2020			2019			2018			2017			2016(1)
Net Asset Value, Beginning of Period	$	12.78		$	11.80		$	12.32		$	12.33		$	10.80
Income (Loss) from Investment Operations:
Net Investment Income(2)		0.32			0.40			0.39			0.34			0.37
Net Realized and Unrealized Gain (Loss)		0.72			1.04			(0.58	)		0.01			1.51
Total from Investment Operations		1.04			1.44			(0.19	)		0.35			1.88
Distributions from and/or in Excess of:
Net Investment Income		(0.33	)		(0.46	)		(0.33	)		(0.36	)		(0.35	)
Net Asset Value, End of Period	$	13.49		$	12.78		$	11.80		$	12.32		$	12.33
Total Return(3)		8.19	%		12.64	%		(1.60	)%		2.95	%(4)		17.79	%(5)
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	182,070		$	122,450		$	108,809		$	37,993		$	31,873
Ratio of Expenses Before Expense Limitation		0.86	%		1.01	%		0.97	%		1.26	%		1.28	%
Ratio of Expenses After Expense Limitation		0.70	%(6)		0.70	%(6)		0.70	%(6)		0.70	%(6)		0.69	%(6)
Ratio of Net Investment Income		2.49	%(6)		3.34	%(6)		3.29	%(6)		2.85	%(6)		3.28	%(6)
Ratio of Rebate from Morgan Stanley Affiliates		0.00	%(7)		0.00	%(7)		0.00	%(7)		0.00	%(7)		0.01	%
Portfolio Turnover Rate		133	%		64	%		37	%		33	%		41	%

(1)  Reflects prior period custodian out-of-pocket expenses that were reimbursed in September 2016. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class I shares. The Ratio of Expenses After Expense Limitation and the Ratio of Net Investment Income would be unchanged as the reimbursement of custodian fees was offset against expense waivers/reimbursements with no impact to net expenses or net investment income.

(2)  Per share amount is based on average shares outstanding.

(3)  Calculated based on the net asset value as of the last business day of the period.

(4)  Performance was positively impacted by approximately 0.85% due to the receipt of proceeds from the settlement of class action suits involving the Fund's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class I shares would have been approximately 2.10%.

(5)  Performance was positively impacted by approximately 9.01% due to the receipt of proceeds from the settlement of class action suits involving the Fund's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class I shares would have been approximately 8.78%.

(6)  The Ratio of Expenses After Expense Limitation and Ratio of Net Investment Income reflect the rebate of certain Fund expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates."

(7)  Amount is less than 0.005%.

The accompanying notes are an integral part of the financial statements.
19

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Corporate Bond Portfolio

	Class A
	Year Ended September 30,
Selected Per Share Data and Ratios	2020			2019			2018			2017			2016(1)
Net Asset Value, Beginning of Period	$	12.80		$	11.81		$	12.32		$	12.34		$	10.81
Income (Loss) from Investment Operations:
Net Investment Income(2)		0.29			0.37			0.33			0.30			0.32
Net Realized and Unrealized Gain (Loss)		0.70			1.04			(0.56	)		(0.00	)(3)		1.53
Total from Investment Operations		0.99			1.41			(0.23	)		0.30			1.85
Distributions from and/or in Excess of:
Net Investment Income		(0.29	)		(0.42	)		(0.28	)		(0.32	)		(0.32	)
Net Asset Value, End of Period	$	13.50		$	12.80		$	11.81		$	12.32		$	12.34
Total Return(4)		7.88	%		12.25	%		(1.87	)%		2.54	%(5)		17.41	%(6)
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	10,807		$	6,400		$	4,496		$	7,911		$	6,916
Ratio of Expenses Before Expense Limitation		1.10	%		1.21	%		1.29	%		1.62	%		1.51	%
Ratio of Expenses After Expense Limitation		0.99	%(7)		0.99	%(7)		1.01	%(7)		1.05	%(7)		0.99	%(7)
Ratio of Net Investment Income		2.20	%(7)		3.04	%(7)		2.78	%(7)		2.50	%(7)		2.78	%(7)
Ratio of Rebate from Morgan Stanley Affiliates		0.00	%(8)		0.00	%(8)		0.00	%(8)		0.00	%(8)		0.01	%
Portfolio Turnover Rate		133	%		64	%		37	%		33	%		41	%

(1)  Reflects prior period custodian out-of-pocket expenses that were reimbursed in September 2016. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class A shares. The Ratio of Expenses After Expense Limitation and the Ratio of Net Investment Income would be unchanged as the reimbursement of custodian fees was offset against expense waivers/reimbursements with no impact to net expenses or net investment income.

(2)  Per share amount is based on average shares outstanding.

(3)  Amount is less than $0.005 per share.

(4)  Calculated based on the net asset value which does not reflect sales charges, if applicable, as of the last business day of the period.

(5)  Performance was positively impacted by approximately 0.85% due to the receipt of proceeds from the settlement of class action suits involving the Fund's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class A shares would have been approximately 1.69%.

(6)  Performance was positively impacted by approximately 8.97% due to the receipt of proceeds from the settlement of class action suits involving the Fund's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class A shares would have been approximately 8.44%.

(7)  The Ratio of Expenses After Expense Limitation and Ratio of Net Investment Income reflect the rebate of certain Fund expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates."

(8)  Amount is less than 0.005%.

The accompanying notes are an integral part of the financial statements.
20

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Corporate Bond Portfolio

	Class L
	Year Ended September 30,
Selected Per Share Data and Ratios	2020			2019			2018			2017			2016(1)
Net Asset Value, Beginning of Period	$	12.79		$	11.79		$	12.30		$	12.32		$	10.79
Income (Loss) from Investment Operations:
Net Investment Income(2)		0.24			0.32			0.29			0.26			0.30
Net Realized and Unrealized Gain (Loss)		0.70			1.04			(0.56	)		(0.00	)(3)		1.51
Total from Investment Operations		0.94			1.36			(0.27	)		0.26			1.81
Distributions from and/or in Excess of:
Net Investment Income		(0.24	)		(0.36	)		(0.24	)		(0.28	)		(0.28	)
Net Asset Value, End of Period	$	13.49		$	12.79		$	11.79		$	12.30		$	12.32
Total Return(4)		7.47	%		11.82	%		(2.19	)%		2.20	%(5)		17.06	%(6)
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	1,727		$	1,671		$	1,499		$	1,749		$	2,151
Ratio of Expenses Before Expense Limitation		1.39	%		1.49	%		1.56	%		1.80	%		1.75	%
Ratio of Expenses After Expense Limitation		1.38	%(7)		1.38	%(7)		1.38	%(7)		1.34	%(7)		1.33	%(7)
Ratio of Net Investment Income		1.84	%(7)		2.67	%(7)		2.45	%(7)		2.20	%(7)		2.64	%(7)
Ratio of Rebate from Morgan Stanley Affiliates		0.00	%(8)		0.00	%(8)		0.00	%(8)		0.01	%		0.01	%
Portfolio Turnover Rate		133	%		64	%		37	%		33	%		41	%

(1)  Reflects prior period custodian out-of-pocket expenses that were reimbursed in September 2016. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class L shares. The Ratio of Expenses After Expense Limitation and the Ratio of Net Investment Income would be unchanged as the reimbursement of custodian fees was offset against expense waivers/reimbursements with no impact to net expenses or net investment income.

(2)  Per share amount is based on average shares outstanding.

(3)  Amount is less than $0.005 per share.

(4)  Calculated based on the net asset value as of the last business day of the period.

(5)  Performance was positively impacted by approximately 0.84% due to the receipt of proceeds from the settlement of class action suits involving the Fund's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class L shares would have been approximately 1.36%.

(6)  Performance was positively impacted by approximately 9.05% due to the receipt of proceeds from the settlement of class action suits involving the Fund's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class L shares would have been approximately 8.01%.

(7)  The Ratio of Expenses After Expense Limitation and Ratio of Net Investment Income reflect the rebate of certain Fund expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates."

(8)  Amount is less than 0.005%.

The accompanying notes are an integral part of the financial statements.
21

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Corporate Bond Portfolio

	Class C
	Year Ended September 30,
Selected Per Share Data and Ratios	2020			2019			2018			2017			2016(1)
Net Asset Value, Beginning of Period	$	12.71		$	11.72		$	12.25		$	12.27		$	10.77
Income (Loss) from Investment Operations:
Net Investment Income(2)		0.18			0.27			0.25			0.21			0.22
Net Realized and Unrealized Gain (Loss)		0.71			1.03			(0.57	)		0.00	(3)		1.53
Total from Investment Operations		0.89			1.30			(0.32	)		0.21			1.75
Distributions from and/or in Excess of:
Net Investment Income		(0.19	)		(0.31	)		(0.21	)		(0.23	)		(0.25	)
Net Asset Value, End of Period	$	13.41		$	12.71		$	11.72		$	12.25		$	12.27
Total Return(4)		7.09	%		11.34	%		(2.64	)%		1.81	%(5)		16.47	%(6)
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	3,222		$	2,801		$	2,074		$	1,084		$	126
Ratio of Expenses Before Expense Limitation		1.90	%		2.01	%		2.15	%		2.82	%		4.45	%
Ratio of Expenses After Expense Limitation		1.80	%(7)		1.80	%(7)		1.80	%(7)		1.80	%(7)		1.79	%(7)
Ratio of Net Investment Income		1.42	%(7)		2.24	%(7)		2.10	%(7)		1.71	%(7)		1.90	%(7)
Ratio of Rebate from Morgan Stanley Affiliates		0.00	%(8)		0.00	%(8)		0.00	%(8)		0.00	%(8)		0.01	%
Portfolio Turnover Rate		133	%		64	%		37	%		33	%		41	%

(1)  Reflects prior period custodian out-of-pocket expenses that were reimbursed in September 2016. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class C shares. The Ratio of Expenses After Expense Limitation and the Ratio of Net Investment Income would be unchanged as the reimbursement of custodian fees was offset against expense waivers/reimbursements with no impact to net expenses or net investment income.

(2)  Per share amount is based on average shares outstanding.

(3)  Amount is less than $0.005 per share.

(4)  Calculated based on the net asset value which does not reflect sales charges, if applicable, as of the last business day of the period.

(5)  Performance was positively impacted by approximately 0.85% due to the receipt of proceeds from the settlement of class action suits involving the Fund's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class C shares would have been approximately 0.96%.

(6)  Performance was positively impacted by approximately 8.85% due to the receipt of proceeds from the settlement of class action suits involving the Fund's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class C shares would have been approximately 7.62%.

(7)  The Ratio of Expenses After Expense Limitation and Ratio of Net Investment Income reflect the rebate of certain Fund expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates."

(8)  Amount is less than 0.005%.

The accompanying notes are an integral part of the financial statements.
22

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements

Morgan Stanley Institutional Fund Trust ("Trust'') is registered under the Investment Company Act of 1940, as amended (the "Act''), as an open-end management investment company. The Trust is comprised of twelve separate, active funds (individually referred to as a "Fund," collectively as the "Funds"). The Trust applies investment company accounting and reporting guidance. All Funds are considered diversified for purposes of the Act.

The accompanying financial statements relate to the Corporate Bond Portfolio. The Fund seeks above-average total return over a market cycle of three to five years. The Fund offers four classes of shares — Class I, Class A, Class L and Class C.

The Fund has suspended offering Class L shares for sale to all investors. Class L shareholders of the Fund do not have the option to purchasing additional Class L shares. However, existing Class L shareholders may invest in additional Class L shares through reinvestment of dividends and distributions.

A. Significant Accounting Policies: The following significant accounting policies are in conformity with U.S. generally accepted accounting principles ("GAAP"). Such policies are consistently followed by the Trust in the preparation of its financial statements. GAAP may require management to make estimates and assumptions that affect the reported amounts and disclosures in the financial statements. Actual results may differ from those estimates.

In March 2017, the Financial Accounting Standards Board ("FASB") issued an Accounting Standard Update, ASU 2017-08, Receivables-Nonrefundable Fees and Other Costs (Subtopic 310-20), Premium Amortization on Purchased Callable Debt Securities ("ASU 2017-08") which amends the amortization period for certain purchased callable debt securities held at a premium, shortening such period to the earliest call date. ASU 2017-08 does not require any accounting change for debt securities held at a discount; the discount continues to be accreted to maturity. ASU 2017-08 is effective for fiscal years, and interim periods within those fiscal years, beginning after December 15, 2018. The adoption resulted in a change in accounting principle, since the Fund had historically amortized such premiums to maturity for U.S. GAAP. Accordingly, the Fund has adopted ASU 2017-08 to amend the premium amortization period for certain purchased callable debt securities with non-contingent call features to the earliest call date. It is impracticable to evaluate the effect on individual prior periods, therefore the Fund applied the amendments on a modified retrospective basis by recognizing a

cumulative effect adjustment that decreased the beginning of period cost of investments and increased the unrealized appreciation on investments of approximately $1,000.

This change in accounting policy has been made to comply with the newly issued accounting standard and had no impact on total accumulated earnings (loss) or the net asset value of the Fund. With respect to the Fund's results of operations, amortization of premium to first call date accelerates amortization with the intent of more closely aligning the recognition of income on such bonds with the economics of the instrument.

In March 2020, FASB issued an Accounting Standard Update, ASU 2020-04, Reference Rate Reform (Topic 848) — Facilitation of the Effects of Reference Rate Reform on Financial Reporting ("ASU 2020-04"), which provides optional, temporary relief with respect to the financial reporting of contracts subject to certain types of modifications due to the planned discontinuation of the London Interbank Offered Rate ("LIBOR") and other IBOR-based reference rates at the end of 2021. The temporary relief provided by ASU 2020-04 is effective for certain reference rate-related contract modifications that occur during the period from March 12, 2020 through December 31, 2022. Management is evaluating the impact of ASU 2020-04 on the Fund's investments, derivatives, debt and other contracts that will undergo reference rate-related modifications as a result of the reference rate reform.

1.  Security Valuation: (1) Certain portfolio securities may be valued by an outside pricing service/vendor approved by the Trust's Board of Trustees (the "Trustees"). The pricing service/vendor may employ a pricing model that takes into account, among other things, bids, yield spreads and/or other market data and specific security characteristics. Alternatively, if a valuation is not available from an outside pricing service/vendor, and the security trades on an exchange, the security may be valued at its latest reported sale price (or at the exchange official closing price if such exchange reports an official closing price), prior to the time when assets are valued. If there are no sales on a given day and if there is no official exchange closing price for that day, the security is valued at the mean between the last reported bid and asked prices if such bid and asked prices are available in the relevant exchanges. If only bid prices are available then the latest bid price may be used. If Morgan Stanley Investment Management Inc. (the "Adviser"), a wholly-owned subsidiary of Morgan Stanley, determines that the price provided by the outside pricing service/vendor or exchange does not reflect the security's

23

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

fair value or is unable to provide a price, prices from brokers or dealers may also be utilized. In these circumstances, the value of the security will be the mean of bid and asked prices obtained from brokers or dealers; (2) futures are valued at the settlement price on the exchange on which they trade or, if a settlement price is unavailable, at the last sale price on the exchange; (3) over-the-counter ("OTC") swaps may be valued by an outside pricing service approved by the Trustees or quotes from a broker or dealer. Swaps cleared on a clearinghouse or exchange may be valued using the closing price provided by the clearinghouse or exchange; (4) when market quotations are not readily available, including circumstances under which the Adviser determines that the closing price, last sale price or the mean between the last reported bid and asked prices are not reflective of a security's market value, portfolio securities are valued at their fair value as determined in good faith under procedures established by and under the general supervision of the Trustees. Occasionally, developments affecting the closing prices of securities and other assets may occur between the times at which valuations of such securities are determined (that is, close of the foreign market on which the securities trade) and the close of business of the New York Stock Exchange ("NYSE"). If developments occur during such periods that are expected to materially affect the value of such securities, such valuations may be adjusted to reflect the estimated fair value of such securities as of the close of the NYSE, as determined in good faith by the Trustees or by the Adviser using a pricing service and/or procedures approved by the Trustees; (5) quotations of foreign portfolio securities, other assets and liabilities and forward contracts stated in foreign currency are translated into U.S. dollar equivalents at the prevailing market rates prior to the close of the NYSE; and (6) investments in mutual funds, including the Morgan Stanley Institutional Liquidity Funds, are valued at the net asset value ("NAV") as of the close of each business day.

The Trustees have responsibility for determining in good faith the fair value of the investments, and the Trustees may appoint others, such as the Trust's Adviser or a valuation committee, to assist the Trustees in determining fair value and to make the actual calculations pursuant to the fair valuation methodologies previously approved by the Trustees. Under procedures approved by the Trustees, the Trust's Adviser has formed a Valuation Committee whose members are approved by the

Trustees. The Valuation Committee provides administration and oversight of the Trust's valuation policies and procedures, which are reviewed at least annually by the Trustees. These procedures allow the Trust to utilize independent pricing services, quotations from securities and financial instrument dealers and other market sources to determine fair value.

2.  Fair Value Measurement: FASB Accounting Standards Codification^TM ("ASC") 820, "Fair Value Measurement" ("ASC 820"), defines fair value as the value that the Fund would receive to sell an investment or pay to transfer a liability in a timely transaction with an independent buyer in the principal market, or in the absence of a principal market, the most advantageous market for the investment or liability. ASC 820 establishes a three-tier hierarchy to distinguish between (1) inputs that reflect the assumptions market participants would use in valuing an asset or liability developed based on market data obtained from sources independent of the reporting entity (observable inputs) and (2) inputs that reflect the reporting entity's own assumptions about the assumptions market participants would use in valuing an asset or liability developed based on the best information available in the circumstances (unobservable inputs) and to establish classification of fair value measurements for disclosure purposes. Various inputs are used in determining the value of the Fund's investments. The inputs are summarized in the three broad levels listed below:

•  Level 1 – unadjusted quoted prices in active markets for identical investments

•  Level 2 – other significant observable inputs (including quoted prices for similar investments, interest rates, prepayment speeds, credit risk, etc.)

•  Level 3 – significant unobservable inputs including the Fund's own assumptions in determining the fair value of investments. Factors considered in making this determination may include, but are not limited to, information obtained by contacting the issuer, analysts, or the appropriate stock exchange (for exchange-traded securities), analysis of the issuer's financial statements or other available documents and, if necessary, available information concerning other securities in similar circumstances.

24

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

The inputs or methodology used for valuing securities are not necessarily an indication of the risk associated with investing in those securities and the determination of the significance of a particular input to the fair value measurement in its entirety requires judgment and considers factors specific to each security.

The following is a summary of the inputs used to value the Fund's investments as of September 30, 2020:

Investment Type	Level 1 Unadjusted quoted prices (000)			Level 2 Other significant observable inputs (000)		Level 3 Significant unobservable inputs (000)		Total (000)
Assets:
Fixed Income Securities
Corporate Bonds	$	—		$	190,001	$	—	$	190,001
Short-Term Investments
Investment Company		9,032			—		—		9,032
U.S. Treasury Security		—			1,864		—		1,864
Total Short-Term Investments		9,032			1,864		—		10,896
Foreign Currency Forward Exchange Contract		—			17		—		17
Futures Contracts		23			—		—		23
Credit Default Swap Agreement		—			52		—		52
Total Assets		9,055			191,934		—		200,989
Liabilities:
Futures Contracts		(208	)		—		—		(208	)
Total	$	8,847		$	191,934	$	—	$	200,781

Transfers between investment levels may occur as the markets fluctuate and/or the availability of data used in an investment's valuation changes.

3.  Foreign Currency Translation and Foreign Investments: The books and records of the Fund are maintained in U.S. dollars. Foreign currency amounts are translated into U.S. dollars as follows:

–  investments, other assets and liabilities at the prevailing rate of exchange on the valuation date;

–  investment transactions and investment income at the prevailing rates of exchange on the dates of such transactions.

Although the net assets of the Fund are presented at the foreign exchange rates and market values at the close of the period, the Fund does not isolate that portion of the results of operations arising as a result of changes in the foreign exchange rates from the fluctuations arising

from changes in the market prices of securities held at period end. Similarly, the Fund does not isolate the effect of changes in foreign exchange rates from the fluctuations arising from changes in the market prices of securities sold during the period. Accordingly, realized and unrealized foreign currency gains (losses) on investments in securities are included in the reported net realized and unrealized gains (losses) on investment transactions and balances. However, pursuant to U.S. federal income tax regulations, gains and losses from certain foreign currency transactions and the foreign currency portion of gains and losses realized on sales and maturities of foreign denominated debt securities are treated as ordinary income for U.S. federal income tax purposes.

Net realized gains (losses) on foreign currency transactions represent net foreign exchange gains (losses) from foreign currency forward exchange contracts, disposition of foreign currency, currency gains (losses) realized between the trade and settlement dates on securities transactions, and the difference between the amount of investment income and foreign withholding taxes recorded on the Fund's books and the U.S. dollar equivalent amounts actually received or paid. The change in unrealized currency gains (losses) on foreign currency transactions for the period is reflected in the Statement of Operations.

Foreign security and currency transactions may involve certain considerations and risks not typically associated with those of U.S. dollar denominated transactions as a result of, among other factors, fluctuations of exchange rates in relation to the U.S. dollar, the possibility of lower levels of governmental supervision and regulation of foreign securities markets and the possibility of political or economic instability.

Governmental approval for foreign investments may be required in advance of making an investment under certain circumstances in some countries, and the extent of foreign investments in domestic companies may be subject to limitation in other countries. Foreign ownership limitations also may be imposed by the charters of individual companies to prevent, among other concerns, violations of foreign investment limitations. As a result, an additional class of shares (identified as "Foreign" in the Portfolio of Investments) may be created and offered for investment. The "local" and "foreign shares" market

25

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

values may differ. In the absence of trading of the foreign shares in such markets, the Fund values the foreign shares at the closing exchange price of the local shares.

4.  Derivatives: The Fund may, but is not required to, use derivative instruments for a variety of purposes, including hedging, risk management, portfolio management or to earn income. Derivatives are financial instruments whose value is based, in part, on the value of an underlying asset, interest rate, index or financial instrument. Prevailing interest rates and volatility levels, among other things, also affect the value of derivative instruments. A derivative instrument often has risks similar to its underlying asset and may have additional risks, including imperfect correlation between the value of the derivative and the underlying asset, risks of default by the counterparty to certain transactions, magnification of losses incurred due to changes in the market value of the securities, instruments, indices or interest rates to which the derivative instrument relates, risks that the transactions may not be liquid and risks arising from margin requirements. The use of derivatives involves risks that are different from, and possibly greater than, the risks associated with other portfolio investments. Derivatives may involve the use of highly specialized instruments that require investment techniques and risk analyses different from those associated with other portfolio investments. All of the Fund's holdings, including derivative instruments, are marked-to-market each day with the change in value reflected in unrealized appreciation (depreciation). Upon disposition, a realized gain or loss is recognized.

Certain derivative transactions may give rise to a form of leverage. Leverage magnifies the potential for gain and the risk of loss. Leverage associated with derivative transactions may cause the Fund to liquidate portfolio positions when it may not be advantageous to do so to satisfy its obligations or to meet earmarking or segregation requirements, pursuant to applicable Securities and Exchange Commission ("SEC") rules and regulations, or may cause the Fund to be more volatile than if the Fund had not been leveraged. Although the Adviser seeks to use derivatives to further the Fund's investment objectives, there is no assurance that the use of derivatives will achieve this result.

Following is a description of the derivative instruments and techniques that the Fund used during the period and their associated risks:

Foreign Currency Forward Exchange Contracts: In connection with its investments in foreign securities, the Fund also entered into contracts with banks, brokers or dealers to purchase or sell securities or foreign currencies at a future date. A foreign currency forward exchange contract ("currency contract") is a negotiated agreement between the contracting parties to exchange a specified amount of currency at a specified future time at a specified rate. The rate can be higher or lower than the spot rate between the currencies that are the subject of the contract. Currency contracts may be used to protect against uncertainty in the level of future foreign currency exchange rates or to gain or modify exposure to a particular currency. In addition, the Fund may use cross currency hedging or proxy hedging with respect to currencies in which the Fund has or expects to have portfolio or currency exposure. Cross currency hedges involve the sale of one currency against the positive exposure to a different currency and may be used for hedging purposes or to establish an active exposure to the exchange rate between any two currencies. To the extent hedged by the use of currency contracts, the precise matching of the currency contract amounts and the value of the securities involved will not generally be possible because the future value of such securities in foreign currencies will change as a consequence of market movements in the value of those securities between the date on which the contract is entered into and the date it matures. Furthermore, such transactions may reduce or preclude the opportunity for gain if the value of the currency should move in the direction opposite to the position taken. There is additional risk to the extent that currency contracts create exposure to currencies in which the Fund's securities are not denominated. Unanticipated changes in currency prices may result in poorer overall performance for the Fund than if it had not entered into such contracts. The use of currency contracts involves the risk of loss from the insolvency or bankruptcy of the counterparty to the contract or the failure of the counterparty to make payments or otherwise comply with the terms of the contract. A currency contract is marked-to-market daily and the change in market value is recorded

26

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

by the Fund as unrealized gain or loss. The Fund records realized gains (losses) when the currency contract is closed equal to the difference between the value of the currency contract at the time it was opened and the value at the time it was closed.

Futures: A futures contract is a standardized, exchange-traded agreement to buy or sell a specific quantity of an underlying asset, reference rate or index at a specific price at a specific future time. The value of a futures contract tends to increase and decrease in tandem with the value of the underlying instrument. Depending on the terms of the particular contract, futures contracts are settled through either physical delivery of the underlying instrument on the settlement date or by payment of a cash settlement amount on the settlement date. During the period the futures contract is open, payments are received from or made to the broker based upon changes in the value of the contract (the variation margin). A decision as to whether, when and how to use futures contracts involves the exercise of skill and judgment and even a well-conceived futures transaction may be unsuccessful because of market behavior or unexpected events. In addition to the derivatives risks discussed above, the prices of futures contracts can be highly volatile, using futures contracts can lower total return and the potential loss from futures contracts can exceed the Fund's initial investment in such contracts. No assurance can be given that a liquid market will exist for any particular futures contract at any particular time. There is also the risk of loss by the Fund of margin deposits in the event of bankruptcy of a broker with which the Fund has open positions in the futures contract.

Swaps: The Fund may enter into OTC swap contracts or cleared swap transactions. A swap contract is an agreement between two parties pursuant to which the parties exchange payments at specified dates on the basis of a specified notional amount, with the payments calculated by reference to specified securities, indices, reference rates, currencies or other instruments. Typically swap agreements provide that when the period payment dates for both parties are the same, the payments are made on a net basis (i.e., the two payment streams are netted out, with only the net amount paid by one party to the other). The Fund's obligations or rights under a swap contract entered into on a net basis will generally be equal only to the net amount to be paid or received

under the agreement, based on the relative values of the positions held by each party. Cleared swap transactions may help reduce counterparty credit risk. In a cleared swap, the Fund's ultimate counterparty is a clearinghouse rather than a swap dealer, bank or other financial institution. OTC swap agreements are not entered into or traded on exchanges and often there is no central clearing or guaranty function for OTC swaps. These OTC swaps are often subject to credit risk or the risk of default or non-performance by the counterparty. Both OTC and cleared swaps could result in losses if interest rates, foreign currency exchange rates or other factors are not correctly anticipated by the Fund or if the reference index, security or investments do not perform as expected. During the period swap agreements are open, payments are received from or made to the clearinghouse or counterparty based upon changes in the value of the contract (variation margin). The Dodd-Frank Wall Street Reform and Consumer Protection Act and related regulatory developments require the clearing and exchange-trading of certain standardized swap transactions. Mandatory exchange-trading and clearing is occurring on a phased-in basis.

The Fund's use of swaps during the period included those based on the credit of an underlying security commonly referred to as "credit default swaps." The Fund may be either the buyer or seller in a credit default swap. Where the Fund is the buyer of a credit default swap contract, it would typically be entitled to receive the par (or other agreed-upon) value of a referenced debt obligation from the counterparty to the contract only in the event of a default or similar event by the issuer of the debt obligation. If no default occurs, the Fund would have paid to the counterparty a periodic stream of payments over the term of the contract and received no benefit from the contract. When the Fund is the seller of a credit default swap contract, it typically receives the stream of payments but is obligated to pay an amount equal to the par (or other agreed-upon) value of a referenced debt obligation upon the default or similar event by the issuer of the referenced debt obligation. The use of credit default swaps could result in losses to the Fund if the Adviser fails to correctly evaluate the creditworthiness of the issuer of the referenced debt obligation.

If the Fund is a seller of protection and a credit event occurs, as defined under the terms of that particular

27

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

swap agreement, the Fund will either (i) pay to the buyer of protection an amount equal to the notional amount of the swap agreement and take delivery of the referenced obligation, other deliverable obligations or underlying securities comprising the referenced index or (ii) pay a net settlement amount in the form of cash or securities equal to the notional amount of the swap agreement less the recovery value of the referenced obligation or underlying securities comprising the referenced index. If the Fund is a buyer of protection and a credit event occurs, as defined under the terms of that particular swap agreement, the Fund will either (i) receive from the seller of protection an amount equal to the notional amount of the swap agreement and deliver the referenced obligation, other deliverable obligations or underlying securities comprising the referenced index or (ii) receive a net settlement amount in the form of cash or securities equal to the notional amount of the swap agreement less the recovery value of the referenced obligation or underlying securities comprising the referenced index. Recovery values are estimated by market makers considering either industry standard recovery rates or entity specific factors and considerations until a credit event occurs. If a credit event has occurred, the recovery value is determined by a facilitated auction whereby a minimum number of allowable broker bids, together with a specified valuation method, are used to calculate the settlement value. The Fund's maximum risk of loss from counterparty risk, either as the protection seller or as the protection buyer, is the fair value of the swap agreement.

The current credit rating of each individual issuer is listed in the table following the Portfolio of Investments and serves as an indicator of the current status of the payment/performance risk of the credit derivative. Alternatively, for credit default swaps on an index of credits, the quoted market prices and current values serve as an indicator of the current status of the payment/performance risk of the credit derivative. Generally, lower credit ratings and increasing market values, in absolute terms, represent a deterioration of the credit and a greater likelihood of an adverse credit event of the issuer.

When the Fund has an unrealized loss on a swap agreement, the Fund has instructed the custodian to pledge cash or liquid securities as collateral with a value approximately equal to the amount of the unrealized loss.

Collateral pledges are monitored and subsequently adjusted if and when the swap valuations fluctuate. If applicable, cash collateral is included with "Due from (to) Broker" in the Statement of Assets and Liabilities.

Upfront payments paid or received by the Fund will be reflected as an asset or liability, respectively, in the Statement of Assets and Liabilities.

FASB ASC 815, "Derivatives and Hedging" ("ASC 815"), is intended to improve financial reporting about derivative instruments by requiring enhanced disclosures to enable investors to better understand how and why the Fund uses derivative instruments, how these derivative instruments are accounted for and their effects on the Fund's financial position and results of operations.

The following tables set forth the fair value of the Fund's derivative contracts by primary risk exposure as of September 30, 2020:

	Asset Derivatives Statement of Assets and Liabilities Location	Primary Risk Exposure	Value (000)
Foreign Currency Forward Exchange Contracts	Unrealized Appreciation on Foreign Currency Forward Exchange Contracts	Currency Risk	$	17
Futures Contracts	Variation Margin on Futures Contracts	Interest Rate Risk		23	(a)
Swap Agreement	Variation Margin on Swap Agreement	Credit Risk		52	(a)
Total			$	92
	Liability Derivatives Statement of Assets and Liabilities Location	Primary Risk Exposure	Value (000)
Futures Contracts	Variation Margin on Futures Contracts	Interest Rate Risk	$	(208	)(a)

(a) This amount represents the cumulative appreciation (depreciation) as reported in the Portfolio of Investments. The Statement of Assets and Liabilities only reflects the current day's net variation margin.

The following tables set forth by primary risk exposure the Fund's realized gains (losses) and change in unrealized appreciation (depreciation) by type of derivative contract for the year ended September 30, 2020 in accordance with ASC 815:

Realized Gain (Loss)
Primary Risk Exposure	Derivative Type	Value (000)
Currency Risk Foreign Currency Forward	Exchange Contracts	$	(76	)
Interest Rate Risk	Futures Contracts		353
Credit Risk	Swap Agreements		90
Interest Rate Risk	Swap Agreements		(1,061	)
Total		$	(694	)

28

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

Change in Unrealized Appreciation (Depreciation)
Primary Risk Exposure	Derivative Type	Value (000)
Currency Risk Foreign Currency Forward	Exchange Contracts	$	17
Interest Rate Risk	Futures Contracts		(21	)
Credit Risk	Swap Agreements		52
Interest Rate Risk	Swap Agreements		494
Total		$	542

At September 30, 2020, the Fund's derivative assets and liabilities are as follows:

Gross Amounts of Assets and Liabilities Presented in the Statement of Assets and Liabilities
Derivatives(b)	Assets(c) (000)		Liabilities(c) (000)
Foreign Currency Forward Exchange Contracts	$	17	$	—

(b) Excludes exchange-traded derivatives.

(c) Absent an event of default or early termination, OTC derivative assets and liabilities are presented gross and not offset in the Statement of Assets and Liabilities.

The Fund typically enters into International Swaps and Derivatives Association, Inc. Master Agreements ("ISDA Master Agreements") or similar master agreements (collectively, "Master Agreements") with its contract counterparties for certain OTC derivatives in order to, among other things, reduce its credit risk to counterparties. ISDA Master Agreements include provisions for general obligations, representations, collateral and events of default or termination. Under an ISDA Master Agreement, the Fund typically may offset with the counterparty certain OTC derivative financial instruments' payables and/or receivables with collateral held and/or posted and create one single net payment (close-out netting) in the event of default, termination and/or potential deterioration in the credit quality of the counterparty. Various Master Agreements govern the terms of certain transactions with counterparties, including transactions such as swap, forward, repurchase and reverse repurchase agreements. These Master Agreements typically attempt to reduce the counterparty risk associated with such transactions by specifying credit protection mechanisms and providing standardization that improves legal certainty. Cross-termination provisions under Master Agreements typically provide that a default in connection with one transaction between the Fund and a counterparty gives the non-defaulting party the right to terminate any other transactions in place with the defaulting party to create one single net payment due to/due from the defaulting party and may be a feature in certain Master Agreements. In the event the Fund exercises its right to terminate a Master Agreement

after a counterparty experiences a termination event as defined in the Master Agreement, the return of collateral with market value in excess of the Fund's net liability may be delayed or denied.

The following table presents derivative financial instruments that are subject to enforceable netting arrangements as of September 30, 2020:

Gross Amounts Not Offset in the Statement of Assets and Liabilities
Counterparty	Gross Asset Derivatives Presented in the Statement of Assets and Liabilities (000)		Financial Instrument (000)		Collateral Received (000)		Net Amount (not less than $0) (000)
Citibank NA	$	17	$	—	$	—	$	17

For the year ended September 30, 2020, the approximate average monthly amount outstanding for each derivative type is as follows:

Foreign Currency Forward Exchange Contracts:
Average monthly principal amount	$	840,000
Futures Contracts:
Average monthly notional value	$	72,277,000
Swap Agreements:
Average monthly notional amount	$	4,444,000

5.  Securities Lending: The Fund lends securities to qualified financial institutions, such as broker-dealers, to earn additional income. Any increase or decrease in the fair value of the securities loaned that might occur and any interest earned or dividends declared on those securities during the term of the loan would remain in the Fund. The Fund would receive cash or securities as collateral in an amount equal to or exceeding 100% of the current fair value of the loaned securities. The collateral is marked-to-market daily by State Street Bank and Trust Company ("State Street"), the securities lending agent, to ensure that a minimum of 100% collateral coverage is maintained.

Based on pre-established guidelines, the securities lending agent invests any cash collateral that is received in an affiliated money market portfolio and repurchase agreements. Securities lending income is generated from the earnings on the invested collateral and borrowing fees, less any rebates owed to the borrowers and compensation to the lending agent, and is recorded as "Income from Securities Loaned — Net" in the Fund's Statement of Operations. Risks in securities lending transactions are that a borrower may not provide additional collateral when required or return the securities when due, and

29

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

that the value of the short-term investments will be less than the amount of cash collateral plus any rebate that is required to be returned to the borrower.

The Fund has the right under the securities lending agreement to recover the securities from the borrower on demand.

The following table presents financial instruments that are subject to enforceable netting arrangements as of September 30, 2020:

Gross Amounts Not Offset in the Statement of Assets and Liabilities
Gross Asset Amounts Presented in the Statement of Assets and Liabilities (000)			Financial Instrument (000)		Collateral Received (000)			Net Amount (not less than $0) (000)
$	3,559	(d)	$	—	$	(3,559	)(e)(f)	$	0

(d) Represents market value of loaned securities at year end.

(e) The Fund received cash collateral of approximately $3,247,000 which was subsequently invested in Morgan Stanley Institutional Liquidity Funds as reported in the Portfolio of Investments. In addition, the Fund received non-cash collateral of approximately $393,000 in the form of U.S. Government obligations, which the Fund cannot sell or repledge, and accordingly are not reflected in the Portfolio of Investments.

(f) The actual collateral received is greater than the amount shown here due to overcollateralization.

FASB ASC 860, "Transfers & Servicing: Repurchase-to-Maturity Transactions, Repurchase Financings, and Disclosures", is intended to provide increased transparency about the types of collateral pledged in securities lending transactions and other similar transactions that are accounted for as secured borrowing.

The following table displays a breakdown of transactions accounted for as secured borrowings, the gross obligations by class of collateral pledged and the remaining contractual maturity of those transactions as of September 30, 2020:

Remaining Contractual Maturity of the Agreements
	Overnight and Continuous (000)		<30 days (000)		Between 30 & 90 days (000)		>90 days (000)		Total (000)
Securities Lending Transactions
Corporate Bonds	$	3,247	$	—	$	—	$	—	$	3,247
Total Borrowings	$	3,247	$	—	$	—	$	—	$	3,247
Gross amount of recognized liabilities for securities lending transactions									$	3,247

6.  When-Issued/Delayed Delivery Securities: The Fund purchases and sells when-issued and delayed delivery securities. Securities purchased on a when-issued or delayed delivery basis are purchased for delivery beyond the normal settlement date at a stated price and yield, and no income accrues to the Fund on such securities prior to delivery date. Payment and delivery for when-issued and delayed delivery securities can take place a month or more after the date of the transaction. When the Fund enters into a purchase transaction on a when-issued or delayed delivery basis, securities are available for collateral in an amount at least equal in value to the Fund's commitments to purchase such securities. Purchasing securities on a when-issued or delayed delivery basis may involve a risk that the market price at the time of delivery may be lower than the agreed upon purchase price, in which case there could be an unrealized loss at the time of delivery. Purchasing investments on a when-issued or delayed delivery basis may be considered a form of leverage which may increase the impact that gains (losses) may have on the Fund.

7.  Indemnifications: The Trust enters into contracts that contain a variety of indemnifications. The Trust's maximum exposure under these arrangements is unknown. However, the Trust has not had prior claims or losses pursuant to these contracts and expects the risk of loss to be remote.

8.  Dividends and Distributions to Shareholders: Dividends and distributions to shareholders are recorded on the ex-dividend date. Dividends from net investment income, if any, are declared and paid monthly. Net realized capital gains, if any, are distributed at least annually.

9.  Security Transactions, Income and Expenses: Security transactions are accounted for on the trade date (date the order to buy or sell is executed). Realized gains and losses on the sale of investment securities are determined on the specific identified cost method. Dividend income and other distributions are recorded on the ex-dividend date (except for certain foreign dividends which may be recorded as soon as the Fund is informed of such dividends) net of applicable withholding taxes. Interest income is recognized on the accrual basis except where collection is in doubt. Discounts are accreted and premiums are amortized over the life of the respective securities. Most expenses of the Trust can be directly attributed to a particular Fund. Expenses which cannot be directly

30

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

attributed are apportioned among the Funds based upon relative net assets or other appropriate methods. Income, expenses (other than class specific expenses — distribution and shareholder services, transfer agency and sub transfer agency fees) and realized and unrealized gains or losses are allocated to each class of shares based upon their relative net assets.

B. Advisory Fees: The Adviser, a wholly-owned subsidiary of Morgan Stanley, provides the Fund with advisory services under the terms of an Investment Advisory Agreement, paid quarterly, at an annual rate of 0.375% of the average daily net assets of the Fund.

The Adviser has agreed to reduce its advisory fee and/or reimburse the Fund so that total annual Fund operating expenses, excluding certain investment related expenses, taxes, interest and other extraordinary expenses (including litigation), will not exceed 0.70% for Class I shares, 1.05% for Class A shares, 1.52% for Class L shares and 1.80% for Class C shares. The fee waivers and/or expense reimbursements will continue for at least one year from the date of the Fund's prospectus or until such time as the Trustees act to discontinue all or a portion of such waivers and/or reimbursements when they deem such action is appropriate. For the year ended September 30, 2020, approximately $9,000 of advisory fees were waived and approximately $215,000 of other expenses were reimbursed by the Adviser pursuant to this arrangement.

C. Administration Fees: The Adviser also serves as Administrator to the Trust and provides administrative services pursuant to an Administration Agreement for an annual fee, accrued daily and paid monthly, of 0.08% of the Fund's average daily net assets. Under a Sub-Administration Agreement between the Administrator and State Street, State Street provides certain administrative services to the Trust. For such services, the Administrator pays State Street a portion of the fee the Administrator receives from the Fund.

D. Distribution and Shareholder Services Fees: Morgan Stanley Distribution, Inc. ("MSDI" or the "Distributor"), a wholly-owned subsidiary of the Adviser, and an indirect subsidiary of Morgan Stanley, serves as the Trust's Distributor of Fund shares pursuant to a Distribution Agreement. The Trust has adopted a Shareholder Services Plan with respect to Class A shares pursuant to Rule 12b-1 under the Act. Under the Shareholder Services Plan, the Fund pays the Distributor a shareholder services fee, accrued daily and paid monthly, at an annual rate of 0.25% of the Fund's average daily net assets attributable to Class A shares. The Distributor

has agreed to waive the 12b-1 fees on Class A shares of the Fund to the extent it exceeds 0.15% of the average daily net assets of such shares on an annualized basis. For the year ended September 30, 2020, this waiver amounted to approximately $8,000.

The Trust has adopted a Distribution and Shareholder Services Plan with respect to Class L shares pursuant to Rule 12b-1 under the Act. Under the Distribution and Shareholder Services Plan, the Fund pays the Distributor a distribution fee, accrued daily and paid monthly, at an annual rate of 0.25% and a shareholder services fee, accrued daily and paid monthly, at an annual rate of 0.25% of the Fund's average daily net assets attributable to Class L shares.

The Trust has adopted a Distribution and Shareholder Services Plan with respect to Class C shares pursuant to Rule 12b-1 under the Act. Under the Distribution and Shareholder Services Plan, the Fund pays the Distributor a distribution fee, accrued daily and paid monthly, at an annual rate of 0.75% and a shareholder services fee, accrued daily and paid monthly, at an annual rate of 0.25% of the Fund's average daily net assets attributable to Class C shares.

The distribution and shareholder services fees are used to support the expenses associated with servicing and maintaining accounts. The Distributor may compensate other parties for providing shareholder support services to investors who purchase Class A, Class L and Class C shares.

E. Dividend Disbursing and Transfer Agent: The Trust's dividend disbursing and transfer agent is DST Asset Manager Solutions, Inc. ("DST"). Pursuant to a Transfer Agency Agreement, the Trust pays DST a fee based on the number of classes, accounts and transactions relating to the Funds of the Trust.

F. Custodian Fees: State Street (the "Custodian") also serves as Custodian for the Trust in accordance with a Custodian Agreement. The Custodian holds cash, securities and other assets of the Trust as required by the Act. Custody fees are payable monthly based on assets held in custody, investment purchases and sales activity and account maintenance fees, plus reimbursement for certain out-of-pocket expenses.

G. Security Transactions and Transactions with Affiliates: For the year ended September 30, 2020, purchases and sales of investment securities for the Fund, other than long-term U.S. Government securities and short-term investments were approximately $251,198,000 and $195,731,000, respectively. There were no purchases and sales of long-term

31

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

U.S. Government securities for the year ended September 30, 2020.

The Fund invests in the Institutional Class of the Morgan Stanley Institutional Liquidity Funds — Government Portfolio (the "Liquidity Funds"), an open-end management investment company managed by the Adviser, both directly and as a portion of the securities held as collateral on loaned securities. Advisory fees paid by the Fund are reduced by an amount equal to its pro-rata share of the advisory and administration fees paid by the Fund due to its investment in the Liquidity Funds. For the year ended September 30, 2020, advisory fees paid were reduced by approximately $5,000 relating to the Fund's investment in the Liquidity Funds.

A summary of the Fund's transactions in shares of affiliated investments during the year ended September 30, 2020 is as follows:

Affiliated Investment Company	Value September 30, 2019 (000)		Purchases at Cost (000)		Proceeds from Sales (000)		Dividend Income (000)
Liquidity Funds	$	6,412	$	85,236	$	82,616	$	24

Affiliated Investment Company (cont'd)	Realized Gain (Loss) (000)		Change in Unrealized Appreciation (Depreciation) (000)		Value September 30, 2020 (000)
Liquidity Funds	$	—	$	—	$	9,032

The Fund is permitted to purchase and sell securities ("cross-trade") from and to other Morgan Stanley funds as well as other funds and client accounts for which the Adviser or an affiliate of the Adviser serves as investment adviser, pursuant to procedures approved by the Trustees in compliance with Rule 17a-7 under the Act (the "Rule"). Each cross-trade is executed at the current market price in compliance with provisions of the Rule. For the year ended September 30, 2020, the Fund did not engage in any cross-trade transactions.

The Fund has an unfunded Deferred Compensation Plan (the "Compensation Plan"), which allows each independent Trustee to defer payment of all, or a portion, of the fees he or she receives for serving on the Board of Trustees. Each eligible Trustee generally may elect to have the deferred amounts credited with a return equal to the total return on one or more of the Morgan Stanley funds that are offered as investment options under the Compensation Plan. Appreciation/depreciation and distributions received from these investments are recorded with an offsetting increase/decrease in the deferred compensation obligation and do not affect the NAV of the Fund.

H. Federal Income Taxes: It is the Fund's intention to continue to qualify as a regulated investment company and distribute all of its taxable and tax-exempt income. Accordingly, no provision for federal income taxes is required in the financial statements.

The Fund may be subject to taxes imposed by countries in which it invests. Such taxes are generally based on income and/or capital gains earned or repatriated. Taxes are accrued based on net investment income, net realized gains and net unrealized appreciation as such income and/or gains are earned. Taxes may also be based on transactions in foreign currency and are accrued based on the value of investments denominated in such currency.

FASB ASC 740-10, "Income Taxes — Overall", sets forth a minimum threshold for financial statement recognition of the benefit of a tax position taken or expected to be taken in a tax return. Management has concluded there are no significant uncertain tax positions that would require recognition in the financial statements. If applicable, the Fund recognizes interest accrued related to unrecognized tax benefits in "Interest Expense" and penalties in "Other Expenses" in the Statement of Operations. The Fund files tax returns with the U.S. Internal Revenue Service, New York and various states. Generally, each of the tax years in the four-year period ended September 30, 2020 remains subject to examination by taxing authorities.

The tax character of distributions paid may differ from the character of distributions shown for GAAP purposes due to short-term capital gains being treated as ordinary income for tax purposes. The tax character of distributions paid during fiscal years 2020 and 2019 was as follows:

2020 Distributions Paid From: Ordinary Income (000)		2019 Distributions Paid From: Ordinary Income (000)
$	3,688	$	4,571

The amount and character of income and gains to be distributed are determined in accordance with income tax regulations which may differ from GAAP. These book/tax differences are either considered temporary or permanent in nature.

Temporary differences are attributable to differing book and tax treatments for the timing of the recognition of gains (losses) on certain investment transactions and the timing of the deductibility of certain expenses.

The Fund had no permanent differences causing reclassifications among the components of net assets for the year ended September 30, 2020.

32

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

At September 30, 2020, the components of distributable earnings for the Fund on a tax basis were as follows:

Undistributed Ordinary Income (000)		Undistributed Long-Term Capital Gain (000)
$	2,479	$	4,127

During the year ended September 30, 2020, the Fund utilized capital loss carryforwards for U. S. federal income tax purposes of approximately $1,265,000.

I. Credit Facility: The Trust and other Morgan Stanley funds participated in a $300,000,000 committed, unsecured revolving line of credit facility (the "Facility") with State Street. This Facility is to be used for temporary emergency purposes or funding of shareholder redemption requests. The interest rate on borrowings is based on the federal funds rate or 1 month LIBOR rate plus a spread. The Facility also has a commitment fee of 0.25% per annum based on the unused portion of the Facility. During the year ended September 30, 2020, the Fund did not have any borrowings under the Facility.

J. Other: At September 30, 2020, the Fund had record owners of 10% or greater. Investment activities of these shareholders could have a material impact on the Fund. The aggregate percentage of such owners was 47.5%.

K. Market Risk: Certain impacts to public health conditions particular to the coronavirus (COVID-19) outbreak could impact the operations and financial performance of certain of the Fund's investments. The extent of the impact to the financial performance of the Fund's investments will depend on future developments, including (i) the duration and spread of the outbreak, (ii) the restrictions and advisories, (iii) the effects on the financial markets, and (iv) the effects on the economy overall, all of which are highly uncertain and cannot be predicted. If the financial performance of the Fund's investments is impacted because of these factors for an extended period, the Fund's investment results may be adversely affected.

L. LIBOR Risk: The Fund's investments, payment obligations and financing terms may be based on floating rates, such as London Interbank Offer Rate ("LIBOR"), Euro Interbank Offered Rate and other similar types of reference rates (each, a "Reference Rate"). These Reference Rates are generally intended to represent the rate at which contributing banks may obtain short-term borrowings from each other within certain financial markets. On July 27, 2017, the Chief Executive of the UK Financial Conduct Authority ("FCA"), which regulates LIBOR, announced that the FCA will no longer persuade

nor require banks to submit rates for the calculation of LIBOR and certain other Reference Rates after 2021. Such announcement indicates that the continuation of LIBOR and other Reference Rates on the current basis cannot and will not be guaranteed after the end of 2021. This announcement and any additional regulatory or market changes may have an adverse impact on the Fund or its investments.

In advance of 2022, regulators and market participants are currently engaged in identifying successor Reference Rates ("Alternative Reference Rates"). Additionally, prior to the end of 2021, it is expected that market participants will focus on the transition mechanisms by which the Reference Rates in existing contracts or instruments may be amended, whether through marketwide protocols, fallback contractual provisions, bespoke negotiations or amendments or otherwise. Nonetheless, the termination of certain Reference Rates presents risks to the Fund. At this time, it is not possible to completely identify or predict the effect of any such changes, any establishment of Alternative Reference Rates or any other reforms to Reference Rates that may be enacted in the UK or elsewhere. The elimination of a Reference Rate or any other changes or reforms to the determination or supervision of Reference Rates could have an adverse impact on the market for or value of any securities or payments linked to those Reference Rates and other financial obligations held by the Fund or on its overall financial condition or results of operations.

33

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Report of Independent Registered Public Accounting Firm

To the Shareholders and Board of Trustees of
Morgan Stanley Institutional Fund Trust —
Corporate Bond Portfolio

Opinion on the Financial Statements

We have audited the accompanying statement of assets and liabilities of Corporate Bond Portfolio (the "Fund") (one of the funds constituting Morgan Stanley Institutional Fund Trust (the "Trust")), including the portfolio of investments, as of September 30, 2020, and the related statement of operations for the year then ended, the statements of changes in net assets for each of the two years in the period then ended, the financial highlights for each of the five years in the period then ended and the related notes (collectively referred to as the "financial statements"). In our opinion, the financial statements present fairly, in all material respects, the financial position of the Fund (one of the funds constituting Morgan Stanley Institutional Fund Trust) at September 30, 2020, the results of its operations for the year then ended, the changes in its net assets for each of the two years in the period then ended and its financial highlights for each of the five years in the period then ended, in conformity with U.S. generally accepted accounting principles.

Basis for Opinion

These financial statements are the responsibility of the Trust's management. Our responsibility is to express an opinion on the Fund's financial statements based on our audits. We are a public accounting firm registered with the Public Company Accounting Oversight Board (United States) ("PCAOB") and are required to be independent with respect to the Trust in accordance with the U.S. federal securities law and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB.

We conducted our audits in accordance with the standards of the PCAOB. Those standards require that we plan and perform the audit to obtain reasonable assurance about whether the financial statements are free of material misstatement, whether due to error or fraud. The Trust is not required to have, nor were we engaged to perform, an audit of the Trust's internal control over financial reporting. As part of our audits we are required to obtain an understanding of internal control over financial reporting but not for the purpose of expressing an opinion on the effectiveness of the Trust's internal control over financial reporting. Accordingly, we express no such opinion.

Our audits included performing procedures to assess the risks of material misstatement of the financial statements, whether due to error or fraud, and performing procedures that respond to those risks. Such procedures included examining, on a test basis, evidence regarding the amounts and disclosures in the financial statements. Our procedures included confirmation of securities owned as of September 30, 2020 by correspondence with the custodian and brokers or by other appropriate auditing procedures where replies from brokers were not received. Our audits also included evaluating the accounting principles used and significant estimates made by management, as well as evaluating the overall presentation of the financial statements. We believe that our audits provide a reasonable basis for our opinion.

We have served as the auditor of one or more Morgan Stanley investment companies since 2000.
Boston, Massachusetts
November 24, 2020

34

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Advisory Agreement Approval (unaudited)

Nature, Extent and Quality of Services

The Board reviewed and considered the nature and extent of the investment advisory services provided by the Adviser under the advisory agreement, including portfolio management, investment research and equity and fixed income securities trading. The Board also reviewed and considered the nature and extent of the non-advisory, administrative services provided by the Administrator under the administration agreement, including accounting, operations, clerical, bookkeeping, compliance, business management and planning, legal services and the provision of supplies, office space and utilities at the Adviser's expense. The Board also considered the Adviser's investment in personnel and infrastructure that benefits the Fund. (The Adviser and Administrator together are referred to as the "Adviser" and the advisory and administration agreements together are referred to as the "Management Agreement.") The Board also considered that the Adviser serves a variety of other investment advisory clients and has experience overseeing service providers. The Board also compared the nature of the services provided by the Adviser with similar services provided by non-affiliated advisers as prepared by Broadridge Financial Solutions, Inc. ("Broadridge").

The Board reviewed and considered the qualifications of the portfolio managers, the senior administrative managers and other key personnel of the Adviser who provide the advisory and administrative services to the Fund. The Board determined that the Adviser's portfolio managers and key personnel are well qualified by education and/or training and experience to perform the services in an efficient and professional manner. The Board concluded that the nature and extent of the advisory and administrative services provided were necessary and appropriate for the conduct of the business and investment activities of the Fund and supported its decision to approve the Management Agreement.

Performance, Fees and Expenses of the Fund

The Board reviewed the performance, fees and expenses of the Fund compared to its peers, as prepared by Broadridge, and to appropriate benchmarks where applicable. The Board discussed with the Adviser the performance goals and the actual results achieved in managing the Fund. When considering a fund's performance, the Board and the Adviser place emphasis on trends and longer-term returns (focusing on one-year, three-year and five-year performance, as of December 31, 2019, or since inception, as applicable). When a fund underperforms its benchmark and/or its peer group average, the Board and the Adviser discuss the causes of such underperformance and, where necessary, they discuss specific changes to investment strategy or investment personnel. The Board noted that the Fund's performance was better than its peer group average for the one-, three- and five-year periods. The Board discussed with the Adviser the level of the advisory and administration fees (together, the "management fee") for this Fund relative to comparable funds and/or other accounts advised by the Adviser and/or compared to its peers as prepared by Broadridge. In addition to the management fee, the Board also reviewed the Fund's total expense ratio. When a fund's management fee and/or its total expense ratio are higher than its peers, the Board and the Adviser discuss the reasons for this and, where appropriate, they discuss possible waivers and/or caps. The Board noted that the Fund's management fee was lower than its peer group average and total expense ratio was higher than its peer group average. After discussion, the Board concluded that the Fund's (i) performance and management fee were competitive with its peer group averages and (ii) total expense ratio was acceptable.

Economies of Scale

The Board considered the size and growth prospects of the Fund and how that relates to the Fund's total expense ratio and particularly the Fund's management fee rate, which does not include breakpoints. In conjunction with its review of the Adviser's profitability, the Board discussed with the Adviser how a change in assets can affect the efficiency or effectiveness of managing the Fund and whether the management fee level is appropriate relative to current and projected asset levels and/or whether the management fee structure reflects economies of scale as asset levels change. The Board has determined that its review of the actual and/or potential economies of scale of the Fund supports its decision to approve the Management Agreement.

Profitability of the Adviser and Affiliates

The Board considered information concerning the costs incurred and profits realized by the Adviser and its affiliates during the last year from their relationship with the Fund and during the last two years from their relationship with the Morgan Stanley Fund Complex and reviewed with the Adviser the cost allocation methodology used to determine the profitability of the Adviser and affiliates. The Board has determined that its review of the analysis of the Adviser's expenses and profitability supports its decision to approve the Management Agreement.

35

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Advisory Agreement Approval (unaudited) (cont'd)

Other Benefits of the Relationship

The Board considered other direct and indirect benefits to the Adviser and/or its affiliates derived from their relationship with the Fund and other funds advised by the Adviser. These benefits may include, among other things, fees for trading, distribution and/or shareholder servicing and for transaction processing and reporting platforms used by securities lending agents, and research received by the Adviser generated from commission dollars spent on funds' portfolio trading. The Board reviewed with the Adviser these arrangements and the reasonableness of the Adviser's costs relative to the services performed. The Board has determined that its review of the other benefits received by the Adviser or its affiliates supports its decision to approve the Management Agreement.

Resources of the Adviser and Historical Relationship Between the Fund and the Adviser

The Board considered whether the Adviser is financially sound and has the resources necessary to perform its obligations under the Management Agreement. The Board also reviewed and considered the historical relationship between the Fund and the Adviser, including the organizational structure of the Adviser, the policies and procedures formulated and adopted by the Adviser for managing the Fund's operations and the Board's confidence in the competence and integrity of the senior managers and key personnel of the Adviser. The Board concluded that the Adviser has the financial resources necessary to fulfill its obligations under the Management Agreement and that it is beneficial for the Fund to continue its relationship with the Adviser.

Other Factors and Current Trends

The Board considered the controls and procedures adopted and implemented by the Adviser and monitored by the Fund's Chief Compliance Officer and concluded that the conduct of business by the Adviser indicates a good faith effort on its part to adhere to high ethical standards in the conduct of the Fund's business.

As part of the Board's review, the Board received information from management on the impact of COVID-19 on the firm generally and the Adviser and the Fund in particular including, among other information, the pandemic's current and expected impact on the Fund's performance and operations.

General Conclusion

After considering and weighing all of the above factors, with various written materials and verbal information presented by the Adviser, the Board concluded that it would be in the best interest of the Fund and its shareholders to approve renewal of the Management Agreement for another year. In reaching this conclusion the Board did not give particular weight to any single piece of information or factor referenced above. The Board considered these factors and information over the course of the year and in numerous meetings, some of which were in executive session with only the independent Board members and their counsel present. It is possible that individual Board members may have weighed these factors, and the information presented, differently in reaching their individual decisions to approve the Management Agreement.

36

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Liquidity Risk Management Program (unaudited)

In compliance with Rule 22e-4 under the Investment Company Act of 1940, as amended (the "Liquidity Rule"), the Fund has adopted and implemented a liquidity risk management program (the "Program"), which is reasonably designed to assess and manage the risk that the Fund could not meet requests to redeem shares issued by the Fund without significant dilution of remaining investors' interests in the Fund (i.e., liquidity risk). The Fund's Board of Trustees (the "Board") previously approved the designation of the Liquidity Risk Subcommittee (the "LRS") as Program administrator. The LRS is comprised of representatives from various divisions within Morgan Stanley Investment Management.

At a meeting held on April 22-23, 2020, the Board reviewed a written report prepared by the LRS that addressed the Program's operation and assessed its adequacy, and effectiveness of implementation for the period from December 1, 2018, through December 31, 2019, as required under the Liquidity Rule. The report concluded that the Program operated effectively and was adequately and effectively implemented in all material aspects, and that the relevant controls and safeguards were appropriately designed to enable the LRS to administer the Program in compliance with the Liquidity Rule.

In accordance with the Program, the LRS assessed each Fund's liquidity risk no less frequently than annually taking into consideration certain factors, as applicable, such as (i) investment strategy and liquidity of portfolio investments, (ii) short-term and long-term cash flow projections and (iii) holdings of cash and cash equivalents and borrowing arrangements and other funding sources. Certain factors are considered under both normal and reasonably foreseeable stressed conditions.

Each Fund portfolio investment is classified into one of four liquidity categories, which classification is assessed at least monthly by the LRS. The classification is based on a determination of the number of days it is reasonably expected to take to convert the investment into cash, or sell or dispose of the investment, in current market conditions without significantly changing the market value of the investment. Liquidity classification determinations take into account various market, trading and investment-specific considerations, as well as market depth, and in some cases utilize third-party vendor data.

The Liquidity Rule limits a fund's investments in illiquid investments to 15% of its net assets and requires funds that do not primarily hold assets that are highly liquid investments to determine and maintain a minimum percentage of the fund's net assets to be invested in highly liquid investments (highly liquid investment minimum or "HLIM"). The LRS believes that the Program includes provisions reasonably designed to review, monitor and comply with the 15% limit on illiquid investments and for determining, periodically reviewing and complying with the HLIM requirement, as applicable.

There can be no assurance that the Program will achieve its objectives under all circumstances in the future. Please refer to the Fund's prospectus for more information regarding the Fund's exposure to liquidity risk and other risks to which it may be subject.

37

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Privacy Notice (unaudited)  April 2019

FACTS	WHAT DOES MSIM DO WITH YOUR PERSONAL INFORMATION?
Why?	Financial companies choose how they share your personal information. Federal law gives consumers the right to limit some but not all sharing. Federal law also requires us to tell you how we collect, share, and protect your personal information. Please read this notice carefully to understand what we do.
What?	The types of personal information we collect and share depend on the product or service you have with us. This information can include: n Social Security number and income n investment experience and risk tolerance n checking account number and wire transfer instructions
How?	All financial companies need to share customers' personal information to run their everyday business. In the section below, we list the reasons financial companies can share their customers' personal information; the reasons MSIM chooses to share; and whether you can limit this sharing.

Reasons we can share your personal information	Does MSIM share?	Can you limit this sharing?
For our everyday business purposes — such as to process your transactions, maintain your account(s), respond to court orders and legal investigations, or report to credit bureaus	Yes	No
For our marketing purposes — to offer our products and services to you	Yes	No
For joint marketing with other financial companies	No	We don't share
For our affiliates' everyday business purposes — information about your transactions and experiences	Yes	No
For our affiliates' everyday business purposes — information about your creditworthiness	No	We don't share
For our affiliates to market to you	No	We don't share
For non-affiliates to market to you	No	We don't share

Questions?Call toll-free (844) 312-6327 or email: imprivacyinquiries@morganstanley.com

38

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Privacy Notice (unaudited) (cont'd)  April 2019

Who we are

Who is providing this notice? Morgan Stanley Investment Management, Inc. and its affiliated registered investment advisers, registered broker-dealers, and registered and unregistered funds ("MSIM")

What we do

How does MSIM protect my personal information?	To protect your personal information from unauthorized access and use, we use security measures that comply with federal law. These measures include computer safeguards and secured files and buildings. We have policies governing the proper handling of customer information by personnel and requiring third parties that provide support to adhere to appropriate security standards with respect to such information.
How does MSIM collect my personal information?	We collect your personal information, for example, when you n open an account or make deposits or withdrawals from your account n buy securities from us or make a wire transfer n give us your contact information We also collect your personal information from others, such as credit bureaus, affiliates, or other companies.
Why can't I limit all sharing?	Federal law gives you the right to limit only n sharing for affiliates' everyday business purposes — information about your creditworthiness n affiliates from using your information to market to you n sharing for non-affiliates to market to you State laws and individual companies may give you additional rights to limit sharing. See below for more on your rights under state law.

Definitions

Affiliates	Companies related by common ownership or control. They can be financial and non-financial companies. n Our affiliates include companies with a Morgan Stanley name and financial companies such as Morgan Stanley Smith Barney LLC and Morgan Stanley & Co.
Non-affiliates	Companies not related by common ownership or control. They can be financial and non-financial companies. n MSIM does not share with non-affiliates so they can market to you.
Joint marketing	A formal agreement between non-affiliated financial companies that together market financial products or services to you. n MSIM doesn't jointly market

Other Important Information

Vermont: Except as permitted by law, we will not share personal information we collect about Vermont residents with Non-affiliates unless you provide us with your written consent to share such information.

California: Except as permitted by law, we will not share personal information we collect about California residents with Non-affiliates and we will limit sharing such personal information with our Affiliates to comply with California privacy laws that apply to us.

39

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited)

Independent Trustees:

Name, Address and Birth Year of Independent Trustee	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years and Other Relevant Professional Experience	Number of Funds in Fund Complex Overseen by Independent Trustee**		Other Directorships Held by Independent Trustee***
Frank L. Bowman c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1944	Trustee	Since August 2006	President, Strategic Decisions, LLC (consulting) (since February 2009); Director or Trustee of various Morgan Stanley Funds (since August 2006); Chairperson of the Compliance and Insurance Committee (since October 2015); formerly, Chairperson of the Insurance Sub-Committee of the Compliance and Insurance Committee (2007-2015); served as President and Chief Executive Officer of the Nuclear Energy Institute (policy organization) (February 2005-November 2008); retired as Admiral, U.S. Navy after serving over 38 years on active duty including 8 years as Director of the Naval Nuclear Propulsion Program in the Department of the Navy and the U.S. Department of Energy (1996-2004); served as Chief of Naval Personnel (July 1994-September 1996) and on the Joint Staff as Director of Political Military Affairs (June 1992-July 1994); knighted as Honorary Knight Commander of the Most Excellent Order of the British Empire; awarded the Officier de l'Orde National du Mérite by the French Government; elected to the National Academy of Engineering (2009).		86	Director of Naval and Nuclear Technologies LLP; Director Emeritus of the Armed Services YMCA; Member of the National Security Advisory Council of the Center for U.S. Global Engagement and a member of the CNA Military Advisory Board; Trustee of Fairhaven United Methodist Church; Member of the Board of Advisors of the Dolphin Scholarship Foundation; Director of other various non-profit organizations; Formerly, Director of BP p.l.c. (November 2010-May 2019).
Kathleen A. Dennis c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1953	Trustee	Since August 2006	President, Cedarwood Associates (mutual fund and investment management consulting) (since July 2006); Chairperson of the Liquidity and Alternatives Sub-Committee of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 2006); formerly, Senior Managing Director of Victory Capital Management (1993-2006).		86	Director of various non-profit organizations.
Nancy C. Everett c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1955	Trustee	Since January 2015	Chief Executive Officer, Virginia Commonwealth University Investment Company (since November 2015); Owner, OBIR, LLC (institutional investment management consulting) (since June 2014); formerly, Managing Director, BlackRock, Inc. (February 2011-December 2013); and Chief Executive Officer, General Motors Asset Management (a/k/a Promark Global Advisors, Inc.) (June 2005-May 2010).		87	Formerly, Member of Virginia Commonwealth University School of Business Foundation (2005-2016); Member of Virginia Commonwealth University Board of Visitors (2013-2015); Member of Committee on Directors for Emerging Markets Growth Fund, Inc. (2007-2010); Chairperson of Performance Equity Management, LLC (2006-2010); and Chairperson, GMAM Absolute Return Strategies Fund, LLC (2006-2010).

40

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Address and Birth Year of Independent Trustee	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years and Other Relevant Professional Experience	Number of Funds in Fund Complex Overseen by Independent Trustee**		Other Directorships Held by Independent Trustee***
Jakki L. Haussler c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1957	Trustee	Since January 2015	Chairman, Opus Capital Group (since January 1996); formerly, Chief Executive Officer, Opus Capital Group (1996-2019); Director, Capvest Venture Fund, LP (May 2000-December 2011); Partner, Adena Ventures, LP (July 1999-December 2010); Director, The Victory Funds (February 2005-July 2008).		87	Director of Service Corporation International and Member, Audit Committee and Investment Committee; Director of Cincinnati Bell Inc. and Member, Audit Committee and Governance and Nominating Committee; Director of Northern Kentucky University Foundation and Member, Investment Committee; Member of Chase College of Law Transactional Law Practice Center Board of Advisors; Director of Chase College of Law Board of Visitors; formerly, Member, University of Cincinnati Foundation Investment Committee; Member, Miami University Board of Visitors (2008-2011); Trustee of Victory Funds (2005-2008) and Chairman, Investment Committee (2007-2008); Member, Service Provider Committee (2005-2008) and Director of Best Transport (2006-2019).
Dr. Manuel H. Johnson c/o Johnson Smick International, Inc. 220 I Street, NE — Suite 200 Washington, D.C. 20002 Birth Year 1949	Trustee	Since July 1991	Senior Partner, Johnson Smick International, Inc. (consulting firm); Chairperson of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since July 1991); Co-Chairman and a founder of the Group of Seven Council (G7C) (international economic commission); formerly, Chairperson of the Audit Committee (July 1991-September 2006), Vice Chairman of the Board of Governors of the Federal Reserve System and Assistant Secretary of the U.S. Treasury.		86	Director of NVR, Inc. (home construction).
Joseph J. Kearns c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1942	Trustee	Since August 1994	Senior Adviser, Kearns & Associates LLC (investment consulting); Chairperson of the Audit Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 1994); Director, Rubicorn Investments (since February 2019); formerly, Deputy Chairperson of the Audit Committee (July 2003-September 2006) and Chairperson of the Audit Committee of various Morgan Stanley Funds (since August 1994); CFO of the J. Paul Getty Trust (1982-1999).		87	Prior to August 10, 2016, Director of Electro Rent Corporation (equipment leasing); Prior to December 31, 2013, Director of The Ford Family Foundation.

41

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Address and Birth Year of Independent Trustee	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years and Other Relevant Professional Experience	Number of Funds in Fund Complex Overseen by Independent Trustee**		Other Directorships Held by Independent Trustee***
Michael F. Klein c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1958	Trustee	Since August 2006	Managing Director, Aetos Alternatives Management, LP (since March 2000); Co-President, Aetos Alternatives Management, LP (since January 2004) and Co-Chief Executive Officer of Aetos Alternatives Management, LP (since August 2013); Chairperson of the Fixed Income Sub-Committee of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 2006); formerly, Managing Director, Morgan Stanley & Co. Inc. and Morgan Stanley Dean Witter Investment Management and President, various Morgan Stanley Funds (June 1998-March 2000); Principal, Morgan Stanley & Co. Inc. and Morgan Stanley Dean Witter Investment Management (August 1997-December 1999).		86	Director of certain investment funds managed or sponsored by Aetos Alternatives Management, LP; Director of Sanitized AG and Sanitized Marketing AG (specialty chemicals).
Patricia Maleski c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1960	Trustee	Since January 2017	Managing Director, JPMorgan Asset Management (2004-2016); Oversight and Control Head of Fiduciary and Conflicts of Interest Program (2015-2016); Chief Control Officer-Global Asset Management (2013-2015); President, JPMorgan Funds (2010-2013); Chief Administrative Officer (2004-2013); various other positions including Treasurer and Board Liaison (since 2001).		87	None.
W. Allen Reed c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1947	Chair of the Board and Trustee	Chair of the Boards since August 2020 and Trustee since August 2006	Chair of the Boards of various Morgan Stanley Funds (since August 2020); Chairperson of the Governance Committee; Chairperson of the Equity Sub-Committee of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 2006); formerly, Vice Chair of the Boards of various Morgan Stanley Funds (January 2020-August 2020); President and Chief Executive Officer of General Motors Asset Management; Chairman and Chief Executive Officer of the GM Trust Bank and Corporate Vice President of General Motors Corporation (August 1994-December 2005).		86	Formerly, Director of Legg Mason, Inc. (2006-2019); and Director of the Auburn University Foundation (2010-2015).

*  This is the earliest date the Trustee began serving the Morgan Stanley Funds. Each Trustee serves an indefinite term, until his or her successor is elected.

**  The Fund Complex includes (as of December 31, 2019) all open-end and closed-end funds (including all of their portfolios) advised by Morgan Stanley Investment Management Inc. (the "Adviser") and any funds that have an adviser that is an affiliated person of the Adviser (including, but not limited to, Morgan Stanley AIP GP LP).

***  This includes any directorships at public companies and registered investment companies held by the Trustee at any time during the past five years.

42

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited) (cont'd)

Executive Officers:

Name, Address and Birth Year of Executive Officer	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years
John H. Gernon 522 Fifth Avenue New York, NY 10036 Birth Year 1963	President and Principal Executive Officer	Since September 2013	President and Principal Executive Officer of the Equity and Fixed Income Funds and the Morgan Stanley AIP Funds (since September 2013) and the Liquidity Funds and various money market funds (since May 2014) in the Fund Complex; Managing Director of the Adviser; Head of Public Markets Product Development (since 2006).
Timothy J. Knierim 522 Fifth Avenue New York, NY 10036 Birth Year 1959	Chief Compliance Officer	Since December 2016	Managing Director of the Adviser and various entities affiliated with the Adviser; Chief Compliance Officer of various Morgan Stanley Funds and the Adviser (since December 2016) and Chief Compliance Officer of Morgan Stanley AIP GP LP (since 2014). Formerly, Managing Director and Deputy Chief Compliance Officer of the Adviser (2014-2016); and formerly, Chief Compliance Officer of Prudential Investment Management, Inc. (2007-2014).
Francis J. Smith 522 Fifth Avenue New York, NY 10036 Birth Year 1965	Treasurer and Principal Financial Officer	Treasurer since July 2003 and Principal Financial Officer since September 2002	Managing Director of the Adviser and various entities affiliated with the Adviser; Treasurer (since July 2003) and Principal Financial Officer of various Morgan Stanley Funds (since September 2002).
Mary E. Mullin 522 Fifth Avenue New York, NY 10036 Birth Year 1967	Secretary	Since June 1999	Managing Director of the Adviser; Secretary of various Morgan Stanley Funds (since June 1999).
Michael J. Key 522 Fifth Avenue New York, NY 10036 Birth Year 1979	Vice President	Since June 2017	Vice President of the Equity and Fixed Income Funds, Liquidity Funds, various money market funds and the Morgan Stanley AIP Funds in the Fund Complex (since June 2017); Executive Director of the Adviser; Head of Product Development for Equity and Fixed Income Funds (since August 2013).

*  This is the earliest date the officer began serving the Morgan Stanley Funds. Each officer serves a one-year term, until his or her successor is elected and qualifies.

43

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Adviser and Administrator

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

Distributor

Morgan Stanley Distribution, Inc.
522 Fifth Avenue
New York, New York 10036

Dividend Disbursing and Transfer Agent

DST Asset Manager Solutions, Inc.
2000 Crown Colony Drive
Quincy, Massachusetts 02169

Custodian

State Street Bank and Trust Company
One Lincoln Street
Boston, Massachusetts 02111

Legal Counsel

Dechert LLP
1095 Avenue of the Americas
New York, New York 10036

Counsel to the Independent Trustees

Perkins Coie LLP
1155 Avenue of the Americas,
22nd Floor
New York, New York 10036

Independent Registered Public Accounting Firm

Ernst & Young LLP
200 Clarendon Street
Boston, Massachusetts 02116

Reporting to Shareholders

Each Morgan Stanley fund provides a complete schedule of portfolio holdings in its Semi-Annual and the Annual Reports within 60 days of the end of the fund's second and fourth fiscal quarters. The Semi-Annual and Annual Reports are filed electronically with the Securities and Exchange Commission ("SEC") on Form N-CSRS and Form N-CSR, respectively. Morgan Stanley also delivers the Semi-Annual and Annual Reports to fund shareholders and makes these reports available on its public website, www.morganstanley.com/im/shareholderreports. Each Morgan Stanley non-money market fund also files a complete schedule of portfolio holdings with the SEC for the fund's first and third fiscal quarters as an attachment to Form N-PORT. Morgan Stanley does not deliver the reports for the first and third fiscal quarters to shareholders, nor are the reports posted to the Morgan Stanley public website. However, the holdings for each money market fund are posted to the Morgan Stanley public website. You may obtain the Form N-PORT filings (as well as the Form N-CSR and N-CSRS filings) by accessing the SEC's website, www.sec.gov. You can also request copies of these materials, upon payment of a duplicating fee, by electronic request at the SEC's email address (publicinfo@sec.gov).

Proxy Voting Policies and Procedures and Proxy Voting Record

You may obtain a copy of the Trust's Proxy Voting Policy and Procedures and information regarding how the Trust voted proxies relating to portfolio securities during the most recent twelve-month period ended June 30, without charge, upon request, by calling toll free 1 (800) 548-7786 or by visiting our website at www.morganstanley.com/im/shareholderreports. This information is also available on the SEC's website at www.sec.gov.

This report is authorized for distribution only when preceded or accompanied by a prospectus or summary prospectus of the applicable Fund of Morgan Stanley Institutional Fund Trust, which describes in detail the Fund's investment policies, risks, fees and expenses. Please read the prospectus carefully before you invest or send money. For additional information, including information regarding the investments comprising the Fund, please visit our website at www.morganstanley.com/im/shareholderreports or call toll free 1 (800) 548-7786.

44

Printed in U.S.A.
This Report has been prepared for shareholders and may be distributed to others only if preceded or accompanied by a current prospectus.

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

© 2020 Morgan Stanley. Morgan Stanley Distribution, Inc.

IFTCBANN
3298799 EXP 11.30.21

INVESTMENT MANAGEMENT

Morgan Stanley Institutional Fund Trust

Discovery Portfolio

Annual Report

September 30, 2020

Beginning on January 1, 2021, as permitted by regulations adopted by the Securities and Exchange Commission ("SEC"), paper copies of the Fund's Annual and Semi-Annual Reports to Shareholders ("Shareholder Reports") will no longer be sent by mail, unless you specifically request paper copies of the Shareholder Reports from the Fund or from your financial intermediary, such as a broker-dealer or a bank. Instead, the Shareholder Reports will be made available on the Fund's website, https://www.morganstanley.com/im/shareholderreports and you will be notified by mail each time a Shareholder Report is posted and provided with a website link to access the Shareholder Report. If you already elected to receive Shareholder Reports electronically, you will not be affected by this change and you need not take any action. You may elect to receive Shareholder Reports and other communications from the Fund electronically anytime by contacting your financial intermediary or, if you are a direct investor, please follow the instructions on the envelope.

Beginning on January 1, 2019, you may elect to receive all future Shareholder Reports in paper free of charge. If you invest through a financial intermediary, you can contact your financial intermediary to request that you continue to receive paper copies of your Shareholder Reports. If you invest directly with the Fund, please follow the instructions on the envelope to let the Fund know you wish to continue receiving paper copies of your Shareholder Reports. Your election to receive Shareholder Reports in paper will apply to all funds held in your account if you invest through your financial intermediary or all funds held with the fund complex if you invest directly with a fund.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Table of Contents

Shareholders' Letter	2
Expense Example	3
Investment Overview	4
Portfolio of Investments	6
Statement of Assets and Liabilities	8
Statement of Operations	10
Statements of Changes in Net Assets	11
Financial Highlights	13
Notes to Financial Statements	18
Report of Independent Registered Public Accounting Firm	28
Investment Advisory Agreement Approval	29
Liquidity Risk Management Program	31
Federal Tax Notice	32
Privacy Notice	33
Trustee and Officer Information	35

This report is authorized for distribution only when preceded or accompanied by a prospectus or summary prospectus of the applicable Fund of the Morgan Stanley Institutional Fund Trust. To receive a prospectus and/or statement of additional information ("SAI"), which contains more complete information such as investment objectives, charges, expenses, policies for voting proxies, risk considerations and describes in detail each of the Fund's investment policies to the prospective investor, please call toll free 1 (800) 548-7786. Please read the prospectuses carefully before you invest or send money.

Additionally, you can access information about the Fund, including performance, characteristics and investment team commentary, through Morgan Stanley Investment Management's website: www.morganstanley.com/im/shareholderreports.

Market forecasts provided in this report may not necessarily come to pass. There is no guarantee that any sectors mentioned will continue to perform as discussed herein or that securities in such sectors will be held by the Fund in the future. There is no assurance that a fund will achieve its investment objective. Funds are subject to market risk, which is the possibility that market values of securities owned by the Fund will decline and, therefore, the value of the Fund's shares may be less than what you paid for them. Accordingly, you can lose money investing in this Fund. Please see the prospectus for more complete information on investment risks.

1

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Shareholders' Letter (unaudited)

Dear Shareholders,

We are pleased to provide this Annual Report, in which you will learn how your investment in Discovery Portfolio (the "Fund") performed during the latest twelve-month period.

Morgan Stanley Investment Management is a client-centric, investor-led organization. Our global presence, intellectual capital, and breadth of products and services enable us to partner with investors to meet the evolving challenges of today's financial markets. We aim to deliver superior investment service and to empower our clients to make the informed decisions that help them reach their investment goals.

As always, we thank you for selecting Morgan Stanley Investment Management, and look forward to working with you in the months and years ahead.

Sincerely,

John H. Gernon
President and Principal Executive Officer

October 2020

2

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Expense Example (unaudited)

Discovery Portfolio

As a shareholder of the Fund, you may incur two types of costs: (1) transactional costs, including sales charge (loads) on purchase payments; and (2) ongoing costs, which may include advisory fees, administration fees, distribution and shareholder services fees; and other Fund expenses. This example is intended to help you understand your ongoing costs (in dollars) of investing in the Fund and to compare these costs with the ongoing costs of investing in other mutual funds.

This example is based on an investment of $1,000 invested at the beginning of the six-month period ended September 30, 2020 and held for the entire six-month period.

Actual Expenses

The table below provides information about actual account values and actual expenses. You may use the information in this table, together with the amount you invested, to estimate the expenses that you paid over the period. Simply divide your account value by $1,000 (for example, an $8,600 account value divided by $1,000 = 8.6), then multiply the result by the number in the table under the heading entitled "Actual Expenses Paid During Period" to estimate the expenses you paid on your account during this period.

Hypothetical Example for Comparison Purposes

The table below provides information about hypothetical account values and hypothetical expenses based on the Fund's actual expense ratio and an assumed rate of return of 5% per year before expenses, which is not the Fund's actual return. The hypothetical account values and expenses may not be used to estimate the actual ending account balance or expenses you paid for the period. You may use this information to compare the ongoing costs of investing in the Fund and other funds. To do so, compare this 5% hypothetical example with the 5% hypothetical examples that appear in the shareholder reports of the other funds.

Please note that the expenses shown in the table are meant to highlight your ongoing costs only and do not reflect any transactional costs, such as sales charges (loads, if applicable). Therefore, the information for each class in the table is useful in comparing ongoing costs only, and will not help you determine the relative total costs of owning different funds. In addition, if these transactional costs were included, your costs would have been higher.

	Beginning Account Value 4/1/20		Actual Ending Account Value 9/30/20		Hypothetical Ending Account Value		Actual Expenses Paid During Period*		Hypothetical Expenses Paid During Period*		Net Expense Ratio During Period**
Discovery Portfolio Class I	$	1,000.00	$	2,121.70	$	1,021.40	$	5.62	$	3.64		0.72	%
Discovery Portfolio Class A		1,000.00		2,119.00		1,020.10		7.64		4.95		0.98
Discovery Portfolio Class L		1,000.00		2,114.40		1,017.65		11.44		7.41		1.47
Discovery Portfolio Class C		1,000.00		2,111.70		1,016.35		13.46		8.72		1.73
Discovery Portfolio Class IS		1,000.00		2,122.80		1,021.90		4.84		3.13		0.62

*  Expenses are calculated using each Fund Class' annualized net expense ratio (as disclosed), multiplied by the average account value over the period and multiplied by 183/366 (to reflect the most recent one-half year period).

**  Annualized.

3

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Overview (unaudited)

Discovery Portfolio

The Fund seeks long-term capital growth.

Performance

For the fiscal year ended September 30, 2020, the Fund's Class I shares had a total return based on net asset value and reinvestment of distributions per share of 115.34%, net of fees. The Fund's Class I shares outperformed against the Fund's benchmark, the Russell Midcap^® Growth Index (the "Index"), which returned 23.23%.

Please keep in mind that triple-digit returns are highly unusual and cannot be sustained. Investors should also be aware that these returns were primarily achieved during favorable market conditions.

Factors Affecting Performance

•  U.S. stocks posted a positive return despite enduring an economic shock and bear market correction caused by a global pandemic. Stock prices fell sharply in February and March 2020 as the measures to contain the spread of COVID-19 stifled economic activity, disrupted supply chains and caused significant job losses. The U.S. government and the Federal Reserve (FED) intervened with aggressive emergency relief, which helped stabilize financial markets. By May, progress toward reducing the coronavirus infection rate allowed the U.S. economy to gradually reopen, leading to a quicker-than-expected rebound in many facets of the economy over the subsequent months. Additionally, COVID-19 vaccine and treatment research was received positively, although the timeline was still uncertain. After recouping all the losses since the February-March 2020 sell-off, the market retreated in September. Investors were unnerved by evidence that the economic recovery was losing momentum amid still high unemployment rates, expiring government aid and an uptick in virus infection rates. Political uncertainty also contributed to increased market volatility due to concerns about a contested presidential election.

•  Counterpoint Global seeks high quality companies, which we define primarily as those with sustainable competitive advantages. We manage concentrated portfolios that are highly differentiated from the benchmark, with securities weighted on our assessment of the quality of the company and our conviction. The value added or detracted in any period of time will result from stock selection, given our philosophy and process.

•  The long-term investment horizon and conviction-weighted investment approach embraced by the team since 1998 can result in periods of performance deviation from the benchmark and peers. The portfolio outperformed the benchmark this reporting period due favorable stock selection and sector allocations.

•  Mid-cap growth stocks advanced 23.23% in the 12-month period, as measured by the Index. Health care, information technology and consumer discretionary were the top performing sectors in the Index, while energy and utilities were the only sectors with negative returns. Against this backdrop, our team continued to focus on stock selection and the long-term outlook for companies in the portfolio.

•  Information technology drove the majority of the portfolio's outperformance this period, primarily due to favorable stock selection. Software and IT services companies were among the largest positive contributors. Investor sentiment broadly remains positive across businesses in the software industry that facilitate virtual collaboration, support distributed workforces, and enable enterprises to improve efficiency, enhance agility, and make more informed data-driven business decisions. Together with the information technology sector, strong stock selection in the consumer discretionary, health care and communication services sectors drove nearly all of the Fund's relative outperformance in the period.

•  Given the Fund's strong outperformance in the period, there were few meaningful detractors from relative performance. An overweight in communication services had a modestly adverse impact on performance, although it was more than offset by the gain from our stock selection in the sector. Stock selection in industrials was another detractor, but the relatively small loss was outweighed by the positive contribution from the Fund's underweight in industrials.

Management Strategies

•  As a team, we believe having a market outlook can be an anchor. Our focus is on assessing company prospects over a five-year horizon and owning a portfolio of unique companies whose market value can increase significantly for underlying fundamental reasons.

4

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Overview (unaudited) (cont'd)

Discovery Portfolio

•  We seek to invest primarily in high-quality established and emerging companies with sustainable competitive advantages, strong free-cash-flow yields and favorable returns on invested capital trends. We focus on long-term growth rather than short-term events, with our stock selection informed by rigorous fundamental analysis.

*  Minimum Investment

In accordance with SEC regulations, the Fund's performance shown assumes that all recurring fees (including management fees) were deducted and all dividends and distributions were reinvested. The performance of Class A, Class L, Class C and Class IS shares will vary from the performance of Class I shares based upon their different inception dates and will be negatively impacted by additional fees assessed to those classes (where applicable).

Performance Compared to the Russell Midcap^® Growth Index⁽¹⁾ and the Lipper Mid-Cap Growth Funds Index⁽²⁾

	Period Ended September 30, 2020 Total Returns(3)
				Average Annual
	One Year			Five Years			Ten Years			Since Inception(9)
Fund — Class I Shares w/o sales charges(4)		115.34	%		31.15	%		18.91	%		15.04	%
Fund — Class A Shares w/o sales charges(5)		114.87			30.78			18.59			13.54
Fund — Class A Shares with maximum 5.25% sales charges(5)		103.63			29.37			17.95			13.28
Fund — Class L Shares w/o sales charges(6)		113.70			30.06			—			21.14
Fund — Class C Shares w/o sales charges(8)		113.21			—			—			43.19
Fund — Class C Shares with maximum 1.00% deferred sales charges(8)		112.21			—			—			43.19
Fund — Class IS Shares w/o sales charges(7)		115.65			31.24			—			21.64
Russell Midcap® Growth Index		23.23			15.53			14.55			10.99
Lipper Mid-Cap Growth Funds Index		23.13			15.38			13.44			10.49

Performance data quoted represents past performance, which is no guarantee of future results, and current performance may be lower or higher than the figures shown. Performance assumes that all dividends and distributions, if any, were reinvested. For the most recent month-end performance figures, please visit www.morganstanley.com/im/shareholderreports. Investment returns and principal value will fluctuate so that Fund shares, when redeemed, may be worth more or less than their original cost. Total returns do not reflect the deduction of taxes that a shareholder would pay on Fund distributions or the redemption of Fund shares. Performance of share classes will vary due to differences in sales charges and expenses.

⁽¹⁾  The Russell Midcap^® Growth Index measures the performance of the mid-cap growth segment of the U.S. equity universe. It includes those Russell Midcap^® Index companies with higher price-to-book ratios and higher forecasted growth values. The Russell Midcap^® Index is a subset of the Russell 1000^® Index and includes approximately 800 of the smallest securities in the Russell 1000^® Index, which in turn consists of approximately 1,000 of the largest U.S. securities based on a combination of market capitalization and current index membership. The Index is unmanaged and its returns do not include any sales charges or fees. Such costs would lower performance. It is not possible to invest directly in an index.

⁽²⁾  The Lipper Mid-Cap Growth Funds Index is an equally weighted performance index of the largest qualifying funds (based on net assets) in the Lipper Mid-Cap Growth Funds classification. The index, which is adjusted for capital gains distributions and income dividends, is unmanaged and should not be considered an investment. There are currently 30 funds represented in this Index. As of the date of this report, the Fund was in the Lipper Mid-Cap Growth Funds classification.

⁽³⁾  Total returns for the Fund reflect expenses waived and/or reimbursed, if applicable, by the Adviser. Without such waivers and/or reimbursements, total returns would have been lower.

⁽⁴⁾  Commenced operations on March 30, 1990.

⁽⁵⁾  Commenced offering on January 31, 1997.

⁽⁶⁾  Commenced offering on June 14, 2012.

⁽⁷⁾  Commenced offering on September 13, 2013.

⁽⁸⁾  Commenced offering on May 31, 2017.

⁽⁹⁾  For comparative purposes, average annual since inception returns listed for the Indexes refer to the inception date of Class I of the Fund, not the inception of the Indexes.

5

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments

Discovery Portfolio

	Shares		Value (000)
Common Stocks (96.0%)
Biotechnology (1.3%)
Alnylam Pharmaceuticals, Inc. (a)		79,156	$	11,525
Exact Sciences Corp. (a)		188,930		19,261
Moderna, Inc. (a)		149,889		10,605
				41,391
Electronic Equipment, Instruments & Components (0.8%)
Cognex Corp.		361,745		23,550
Entertainment (5.2%)
Roku, Inc. (a)		228,706		43,179
Spotify Technology SA (a)		364,158		88,334
Zynga, Inc., Class A (a)		3,220,311		29,369
				160,882
Health Care Equipment & Supplies (4.1%)
DexCom, Inc. (a)		236,822		97,625
Penumbra, Inc. (a)		143,420		27,878
				125,503
Health Care Providers & Services (3.9%)
Covetrus, Inc. (a)		3,250,807		79,319
Guardant Health, Inc. (a)		378,653		42,326
				121,645
Health Care Technology (6.6%)
Agilon Health Topco, Inc.(a)(b)(c) (acquisition cost — $2,693; acquired 11/7/18)		7,122		3,980
GoodRx Holdings, Inc., Class A (a)		693,802		38,575
Livongo Health, Inc. (a)		102,166		14,309
Veeva Systems, Inc., Class A (a)		519,191		145,991
				202,855
Information Technology Services (24.3%)
Adyen N.V. (Netherlands) (a)		26,758		49,355
Fastly, Inc., Class A (a)		1,603,677		150,232
MongoDB, Inc. (a)		613,383		142,004
Okta, Inc. (a)		661,621		141,488
Snowflake, Inc., Class A (a)(d)		41,917		10,521
Square, Inc., Class A (a)		648,961		105,489
Twilio, Inc., Class A (a)		607,839		150,191
				749,280
Interactive Media & Services (10.5%)
Pinterest, Inc., Class A (a)		1,432,990		59,483
Snap, Inc., Class A (a)		2,031,805		53,051
Twitter, Inc. (a)		2,280,490		101,482
Zillow Group, Inc., Class C (a)		537,721		54,627
ZoomInfo Technologies, Inc., Class A (a)		1,282,411		55,131
				323,774
Internet & Direct Marketing Retail (7.5%)
Chewy, Inc., Class A (a)		656,001		35,968
Farfetch Ltd., Class A (a)		1,895,848		47,700
Overstock.com, Inc. (a)		647,488		47,040
Wayfair, Inc., Class A (a)		344,941		100,381
				231,089

	Shares		Value (000)
Leisure Products (2.9%)
Peloton Interactive, Inc., Class A (a)		894,051	$	88,726
Life Sciences Tools & Services (5.2%)
10X Genomics, Inc., Class A (a)		1,294,492		161,397
Metals & Mining (0.1%)
Royal Gold, Inc.		34,063		4,093
Oil, Gas & Consumable Fuels (0.1%)
Texas Pacific Land Trust		8,482		3,830
Pharmaceuticals (1.2%)
Royalty Pharma PLC, Class A (United Kingdom)		906,521		38,137
Semiconductors & Semiconductor Equipment (0.7%)
Teradyne, Inc.		268,507		21,336
Software (17.2%)
Alteryx, Inc., Class A (a)		484,263		54,988
Coupa Software, Inc. (a)		308,470		84,595
Datadog, Inc., Class A (a)		661,139		67,542
DocuSign, Inc. (a)		210,832		45,379
Nuance Communications, Inc. (a)		448,132		14,874
Slack Technologies, Inc., Class A (a)		2,500,217		67,156
Trade Desk, Inc. (The), Class A (a)		211,702		109,827
Unity Software, Inc. (a)		158,672		13,849
Zoom Video Communications, Inc., Class A (a)		155,855		73,269
				531,479
Specialty Retail (4.4%)
Carvana Co. (a)		613,287		136,800
Total Common Stocks (Cost $1,965,846)				2,965,767
Preferred Stocks (0.1%)
Internet & Direct Marketing Retail (0.1%)
Overstock.com, Inc. Series A-1 (a)(d) (Cost $337)		44,025		2,774
Short-Term Investments (3.0%)
Securities held as Collateral on Loaned Securities (0.4%)
Investment Company (0.3%)
Morgan Stanley Institutional Liquidity Funds — Treasury Securities Portfolio — Institutional Class (See Note G)		9,033,000		9,033
	Face Amount (000)
Repurchase Agreements (0.1%)
Barclays Capital, Inc., (0.06%, dated 9/30/20, due 10/1/20; proceeds $1,365; fully collateralized by a U.S. Government obligation; 2.13% due 5/15/22; valued at $1,393)	$	1,365		1,365
Merrill Lynch & Co., Inc., (0.05%, dated 9/30/20, due 10/1/20; proceeds $170; fully collateralized by U.S. Government obligations; 1.50% due 10/31/24; valued at $174)		170		170

The accompanying notes are an integral part of the financial statements.
6

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Discovery Portfolio

	Face Amount (000)		Value (000)
Repurchase Agreements (cont'd)
Merrill Lynch & Co., Inc., (0.06%, dated 9/30/20, due 10/1/20; proceeds $525; fully collateralized by U.S. Government obligations; 1.50% due 10/31/24; valued at $536)	$	525	$	525
				2,060
Total Securities held as Collateral on Loaned Securities (Cost $11,093)				11,093
	Shares
Investment Company (2.6%)
Morgan Stanley Institutional Liquidity Funds — Treasury Securities Portfolio — Institutional Class (See Note G) (Cost $80,688)		80,688,078		80,688
Total Short-Term Investments (Cost $91,781)				91,781
Total Investments Excluding Purchased Options (99.1%) (Cost $2,057,964)				3,060,322
Total Purchased Options Outstanding (0.1%) (Cost $7,331)				3,218
Total Investments (99.2%) (Cost $2,065,295) Including $10,527 of Securities Loaned (e)(f)				3,063,540
Other Assets in Excess of Liabilities (0.8%)				24,969
Net Assets (100.0%)			$	3,088,509

(a)  Non-income producing security.

(b)  At September 30, 2020, the Fund held a fair valued security valued at approximately $3,980,000, representing 0.1% of net assets. This security has been fair valued as determined in good faith under procedures established by and under the general supervision of the Trust's (as defined herein) Trustees.

(c)  Security cannot be offered for public resale without first being registered under the Securities Act of 1933 and related rules ("restricted security"). Acquisition date represents the day on which an enforceable right to acquire such security is obtained and is presented along with related cost in the security description. The Fund has registration rights for certain restricted securities. Any costs related to such registration are borne by the issuer. The aggregate value of restricted securities (excluding 144A holdings) at September 30, 2020 amounts to approximately $3,980,000 and represents 0.1% of net assets.

(d)  All or a portion of this security was on loan at September 30, 2020.

(e)  The approximate fair value and percentage of net assets, $49,355,000 and 1.6%, respectively, represent the securities that have been fair valued under the fair valuation policy for international investments as described in Note A-1 within the Notes to the Financial Statements.

(f)  At September 30, 2020, the aggregate cost for federal income tax purposes is approximately $2,081,996,000. The aggregate gross unrealized appreciation is approximately $1,025,503,000 and the aggregate gross unrealized depreciation is approximately $43,959,000, resulting in net unrealized appreciation of approximately $981,544,000.

Call Options Purchased:

The Fund had the following call options purchased open at September 30, 2020:

Counterparty	Description	Strike Price		Expiration Date	Number of Contracts		Notional Amount (000)		Value (000)		Premiums Paid (000)		Unrealized Depreciation (000)
BNP Paribas	USD/CNH	CNH	7.99	Sep-21		451,174,389		451,174	$	1,654	$	2,732	$	(1,078	)
Royal Bank of Scotland	USD/CNH	CNH	7.75	Jan-21		197,985,615		197,986		124		865		(741	)
Royal Bank of Scotland	USD/CNH	CNH	8.06	Jul-21		437,306,829		437,307		1,197		2,319		(1,122	)
Royal Bank of Scotland	USD/CNH	CNH	8.48	May-21		226,595,778		226,596		243		1,415		(1,172	)
									$	3,218	$	7,331	$	(4,113	)

CNH  —  Chinese Yuan Renminbi Offshore

USD  —  United States Dollar

Portfolio Composition*

Classification	Percentage of Total Investments
Information Technology Services		24.6	%
Other**		22.5
Software		17.4
Interactive Media & Services		10.6
Internet & Direct Marketing Retail		7.7
Health Care Technology		6.6
Life Sciences Tools & Services		5.3
Entertainment		5.3
Total Investments		100.0	%

*  Percentages indicated are based upon total investments (excluding Securities held as Collateral on Loaned Securities) as of September 30, 2020.

**  Industries and/or investment types representing less than 5% of total investments.

The accompanying notes are an integral part of the financial statements.
7

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Discovery Portfolio

Statement of Assets and Liabilities	September 30, 2020 (000)
Assets:
Investments in Securities of Unaffiliated Issuers, at Value(1) (Cost $1,975,574)	$	2,973,819
Investment in Security of Affiliated Issuer, at Value (Cost $89,721)		89,721
Total Investments in Securities, at Value (Cost $2,065,295)		3,063,540
Foreign Currency, at Value (Cost $1)		1
Cash from Securities Lending		—	@
Receivable for Investments Sold		36,234
Receivable for Fund Shares Sold		11,577
Receivable from Securities Lending Income		11
Receivable from Affiliate		1
Other Assets		405
Total Assets		3,111,769
Liabilities:
Collateral on Securities Loaned, at Value		11,093
Payable for Fund Shares Redeemed		3,726
Due to Broker		3,605
Payable for Advisory Fees		3,143
Payable for Investments Purchased		718
Payable for Shareholder Services Fees — Class A		260
Payable for Distribution and Shareholder Services Fees — Class L		8
Payable for Distribution and Shareholder Services Fees — Class C		24
Payable for Sub Transfer Agency Fees — Class I		111
Payable for Sub Transfer Agency Fees — Class A		111
Payable for Sub Transfer Agency Fees — Class L		1
Payable for Sub Transfer Agency Fees — Class C		2
Payable for Administration Fees		186
Payable for Professional Fees		73
Payable for Trustees' Fees and Expenses		41
Payable for Transfer Agency Fees — Class I		5
Payable for Transfer Agency Fees — Class A		10
Payable for Transfer Agency Fees — Class L		1
Payable for Transfer Agency Fees — Class C		1
Payable for Transfer Agency Fees — Class IS		2
Payable for Custodian Fees		12
Other Liabilities		127
Total Liabilities		23,260
Net Assets	$	3,088,509
Net Assets Consist of:
Paid-in-Capital	$	1,858,166
Total Distributable Earnings		1,230,343
Net Assets	$	3,088,509

The accompanying notes are an integral part of the financial statements.
8

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Discovery Portfolio

Statement of Assets and Liabilities (cont'd)	September 30, 2020 (000)
CLASS I:
Net Assets	$	1,282,828
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		33,590,570
Net Asset Value, Offering and Redemption Price Per Share	$	38.19
CLASS A:
Net Assets	$	1,403,660
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		46,919,963
Net Asset Value, Redemption Price Per Share	$	29.92
Maximum Sales Load		5.25	%
Maximum Sales Charge	$	1.66
Maximum Offering Price Per Share	$	31.58
CLASS L:
Net Assets	$	14,173
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		551,764
Net Asset Value, Offering and Redemption Price Per Share	$	25.69
CLASS C:
Net Assets	$	33,781
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		1,175,437
Net Asset Value, Offering and Redemption Price Per Share	$	28.74
CLASS IS:
Net Assets	$	354,067
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		9,145,401
Net Asset Value, Offering and Redemption Price Per Share	$	38.72
(1) Including: Securities on Loan, at Value:	$	10,527

@  Amount is less than $500.

The accompanying notes are an integral part of the financial statements.
9

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Discovery Portfolio

Statement of Operations	Year Ended September 30, 2020 (000)
Investment Income:
Income from Securities Loaned — Net	$	1,706
Dividends from Securities of Unaffiliated Issuers (Net of $5 of Foreign Taxes Withheld)		505
Dividends from Security of Affiliated Issuer (Note G)		192
Total Investment Income		2,403
Expenses:
Advisory Fees (Note B)		7,000
Shareholder Services Fees — Class A (Note D)		1,470
Distribution and Shareholder Services Fees — Class L (Note D)		73
Distribution and Shareholder Services Fees — Class C (Note D)		131
Sub Transfer Agency Fees — Class I		591
Sub Transfer Agency Fees — Class A		640
Sub Transfer Agency Fees — Class L		6
Sub Transfer Agency Fees — Class C		12
Administration Fees (Note C)		1,120
Registration Fees		358
Professional Fees		214
Shareholder Reporting Fees		135
Transfer Agency Fees — Class I (Note E)		20
Transfer Agency Fees — Class A (Note E)		42
Transfer Agency Fees — Class L (Note E)		5
Transfer Agency Fees — Class C (Note E)		3
Transfer Agency Fees — Class IS (Note E)		7
Custodian Fees (Note F)		39
Trustees' Fees and Expenses		23
Pricing Fees		3
Other Expenses		51
Expenses Before Non Operating Expenses		11,943
Bank Overdraft Expense		9
Total Expenses		11,952
Rebate from Morgan Stanley Affiliate (Note G)		(147	)
Net Expenses		11,805
Net Investment Loss		(9,402	)
Realized Gain (Loss):
Investments Sold		256,448
Foreign Currency Translation		(5	)
Net Realized Gain		256,443
Change in Unrealized Appreciation (Depreciation):
Investments		953,720
Foreign Currency Translation		(—	@)
Net Change in Unrealized Appreciation (Depreciation)		953,720
Net Realized Gain and Change in Unrealized Appreciation (Depreciation)		1,210,163
Net Increase in Net Assets Resulting from Operations	$	1,200,761

@  Amount is less than $500.

The accompanying notes are an integral part of the financial statements.
10

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Discovery Portfolio

Statements of Changes in Net Assets	Year Ended September 30, 2020 (000)			Year Ended September 30, 2019 (000)
Increase (Decrease) in Net Assets:
Operations:
Net Investment Loss	$	(9,402	)	$	(2,925	)
Net Realized Gain		256,443			134,151
Net Change in Unrealized Appreciation (Depreciation)		953,720			(123,664	)
Net Increase in Net Assets Resulting from Operations		1,200,761			7,562
Dividends and Distributions to Shareholders:
Class I		(37,434	)		(47,434	)
Class A		(47,691	)		(56,202	)
Class L		(1,239	)		(1,904	)
Class C		(1,011	)		(138	)
Class IS		(14,656	)		(15,697	)
Total Dividends and Distributions to Shareholders		(102,031	)		(121,375	)
Capital Share Transactions:(1)
Class I:
Subscribed		724,696			233,979
Distributions Reinvested		37,394			47,059
Redeemed		(344,262	)		(169,311	)
Class A:
Subscribed		894,159			269,839
Distributions Reinvested		47,483			55,847
Redeemed		(380,841	)		(167,362	)
Class L:
Exchanged		117			28
Distributions Reinvested		1,231			1,883
Redeemed		(1,927	)		(1,677	)
Class C:
Subscribed		18,597			7,204
Distributions Reinvested		1,003			136
Redeemed		(2,622	)		(1,047	)
Class IS:
Subscribed		138,795			51,205
Distributions Reinvested		14,656			15,694
Redeemed		(82,016	)		(18,561	)
Net Increase in Net Assets Resulting from Capital Share Transactions		1,066,463			324,916
Total Increase in Net Assets		2,165,193			211,103
Net Assets:
Beginning of Period		923,316			712,213
End of Period	$	3,088,509		$	923,316

The accompanying notes are an integral part of the financial statements.
11

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Discovery Portfolio

Statements of Changes in Net Assets (cont'd)	Year Ended September 30, 2020 (000)			Year Ended September 30, 2019 (000)
(1)   Capital Share Transactions:
Class I:
Shares Subscribed		26,530			11,358
Shares Issued on Distributions Reinvested		1,994			2,875
Shares Redeemed		(13,746	)		(8,473	)
Net Increase in Class I Shares Outstanding		14,778			5,760
Class A:
Shares Subscribed		37,384			15,741
Shares Issued on Distributions Reinvested		3,226			4,208
Shares Redeemed		(18,715	)		(10,392	)
Net Increase in Class A Shares Outstanding		21,895			9,557
Class L:
Shares Exchanged		6			2
Shares Issued on Distributions Reinvested		97			160
Shares Redeemed		(123	)		(123	)
Net Increase (Decrease) in Class L Shares Outstanding		(20	)		39
Class C:
Shares Subscribed		833			448
Shares Issued on Distributions Reinvested		71			10
Shares Redeemed		(145	)		(70	)
Net Increase in Class C Shares Outstanding		759			388
Class IS:
Shares Subscribed		4,897			2,482
Shares Issued on Distributions Reinvested		772			949
Shares Redeemed		(3,009	)		(902	)
Net Increase in Class IS Shares Outstanding		2,660			2,529

The accompanying notes are an integral part of the financial statements.
12

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Discovery Portfolio

	Class I
	Year Ended September 30,
Selected Per Share Data and Ratios	2020			2019			2018			2017			2016(1)
Net Asset Value, Beginning of Period	$	19.92		$	23.30		$	22.30		$	31.85		$	35.96
Income (Loss) from Investment Operations:
Net Investment Income (Loss)(2)		(0.15	)		(0.05	)		(0.07	)		0.05			0.03
Net Realized and Unrealized Gain		20.73			0.35			7.99			1.99			0.18
Total from Investment Operations		20.58			0.30			7.92			2.04			0.21
Distributions from and/or in Excess of:
Net Realized Gain		(2.31	)		(3.68	)		(6.92	)		(11.59	)		(4.32	)
Net Asset Value, End of Period	$	38.19		$	19.92		$	23.30		$	22.30		$	31.85
Total Return(3)		115.34	%		4.71	%		47.85	%		16.16	%		0.19	%
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	1,282,828		$	374,736		$	304,179		$	242,140		$	563,397
Ratio of Expenses Before Expense Limitation		0.74	%		0.74	%		0.72	%		0.72	%		0.74	%
Ratio of Expenses After Expense Limitation		0.73	%(4)		0.73	%(4)		0.71	%(4)		0.72	%(4)		0.73	%(4)
Ratio of Expenses After Expense Limitation Excluding Non-Operating Expenses		0.73	%(4)		0.73	%(4)		0.71	%(4)		0.71	%(4)		N/A
Ratio of Net Investment Income (Loss)		(0.57	)%(4)		(0.27	)%(4)		(0.35	)%(4)		0.21	%(4)		0.09	%(4)
Ratio of Rebate from Morgan Stanley Affiliates		0.01	%		0.01	%		0.01	%		0.01	%		0.00	%(5)
Portfolio Turnover Rate		65	%		116	%		86	%		59	%		23	%

(1)  Reflects prior period custodian out-of-pocket expenses that were reimbursed in September 2016. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class I shares. The Ratio of Expenses After Expense Limitation would have been 0.005% higher and the Ratio of Net Investment Income would have been 0.005% lower had the custodian not reimbursed the Fund.

(2)  Per share amount is based on average shares outstanding.

(3)  Calculated based on the net asset value as of the last business day of the period.

(4)  The Ratio of Expenses After Expense Limitation and Ratio of Net Investment Income (Loss) reflect the rebate of certain Fund expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates."

(5)  Amount is less than 0.005%.

The accompanying notes are an integral part of the financial statements.
13

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Discovery Portfolio

	Class A
	Year Ended September 30,
Selected Per Share Data and Ratios	2020			2019			2018			2017			2016(1)
Net Asset Value, Beginning of Period	$	16.12		$	19.71		$	19.92		$	29.86		$	34.06
Income (Loss) from Investment Operations:
Net Investment Loss(2)		(0.17	)		(0.09	)		(0.11	)		(0.03	)		(0.05	)
Net Realized and Unrealized Gain		16.28			0.18			6.82			1.68			0.17
Total from Investment Operations		16.11			0.09			6.71			1.65			0.12
Distributions from and/or in Excess of:
Net Realized Gain		(2.31	)		(3.68	)		(6.92	)		(11.59	)		(4.32	)
Net Asset Value, End of Period	$	29.92		$	16.12		$	19.71		$	19.92		$	29.86
Total Return(3)		114.87	%		4.40	%		47.36	%		15.85	%		(0.12	)%
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	1,403,660		$	403,285		$	304,921		$	289,123		$	480,488
Ratio of Expenses Before Expense Limitation		1.01	%		1.00	%		1.02	%		1.01	%		1.00	%
Ratio of Expenses After Expense Limitation		1.00	%(4)		0.99	%(4)		1.01	%(4)		1.01	%(4)		0.99	%(4)
Ratio of Expenses After Expense Limitation Excluding Non-Operating Expenses		1.00	%(4)		0.99	%(4)		1.01	%(4)		1.00	%(4)		N/A
Ratio of Net Investment Loss		(0.82	)%(4)		(0.52	)%(4)		(0.65	)%(4)		(0.17	)%(4)		(0.17	)%(4)
Ratio of Rebate from Morgan Stanley Affiliates		0.01	%		0.01	%		0.01	%		0.01	%		0.00	%(5)
Portfolio Turnover Rate		65	%		116	%		86	%		59	%		23	%

(1)  Reflects prior period custodian out-of-pocket expenses that were reimbursed in September 2016. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class A shares. The Ratio of Expenses After Expense Limitation would have been less than 0.005% higher and the Ratio of Net Investment Loss would have been less than 0.005% lower had the custodian not reimbursed the Fund.

(2)  Per share amount is based on average shares outstanding.

(3)  Calculated based on the net asset value which does not reflect sales charges, if applicable, as of the last business day of the period.

(4)  The Ratio of Expenses After Expense Limitation and Ratio of Net Investment Loss reflect the rebate of certain Fund expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates."

(5)  Amount is less than 0.005%.

The accompanying notes are an integral part of the financial statements.
14

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Discovery Portfolio

	Class L
	Year Ended September 30,
Selected Per Share Data and Ratios	2020			2019			2018			2017			2016(1)
Net Asset Value, Beginning of Period	$	14.21		$	17.96		$	18.79		$	29.01		$	33.39
Income (Loss) from Investment Operations:
Net Investment Loss(2)		(0.21	)		(0.15	)		(0.18	)		(0.16	)		(0.22	)
Net Realized and Unrealized Gain		14.00			0.08			6.27			1.53			0.16
Total from Investment Operations		13.79			(0.07	)		6.09			1.37			(0.06	)
Distributions from and/or in Excess of:
Net Realized Gain		(2.31	)		(3.68	)		(6.92	)		(11.59	)		(4.32	)
Net Asset Value, End of Period	$	25.69		$	14.21		$	17.96		$	18.79		$	29.01
Total Return(3)		113.70	%		3.90	%		46.73	%		15.07	%		(0.73	)%
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	14,173		$	8,124		$	9,572		$	8,091		$	9,874
Ratio of Expenses Before Expense Limitation		1.50	%		1.51	%		1.51	%		1.64	%		1.61	%
Ratio of Expenses After Expense Limitation		1.49	%(4)		1.50	%(4)		1.50	%(4)		1.63	%(4)		1.60	%(4)
Ratio of Expenses After Expense Limitation Excluding Non-Operating Expenses		1.49	%(4)		1.50	%(4)		1.50	%(4)		1.63	%(4)		N/A
Ratio of Net Investment Loss		(1.27	)%(4)		(1.06	)%(4)		(1.15	)%(4)		(0.85	)%(4)		(0.76	)%(4)
Ratio of Rebate from Morgan Stanley Affiliates		0.01	%		0.01	%		0.01	%		0.01	%		0.00	%(5)
Portfolio Turnover Rate		65	%		116	%		86	%		59	%		23	%

(1)  Reflects prior period custodian out-of-pocket expenses that were reimbursed in September 2016. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class L shares. The Ratio of Expenses After Expense Limitation would have been less than 0.005% higher and the Ratio of Net Investment Loss would have been less than 0.005% lower had the custodian not reimbursed the Fund.

(2)  Per share amount is based on average shares outstanding.

(3)  Calculated based on the net asset value as of the last business day of the period.

(4)  The Ratio of Expenses After Expense Limitation and Ratio of Net Investment Loss reflect the rebate of certain Fund expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates."

(5)  Amount is less than 0.005%.

The accompanying notes are an integral part of the financial statements.
15

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Discovery Portfolio

	Class C
	Year Ended September 30,									Period from May 31, 2017(1) to
Selected Per Share Data and Ratios	2020			2019			2018			September 30, 2017
Net Asset Value, Beginning of Period	$	15.67		$	19.42		$	19.85		$	19.34
Income (Loss) from Investment Operations:
Net Investment Loss(2)		(0.32	)		(0.22	)		(0.29	)		(0.09	)
Net Realized and Unrealized Gain		15.70			0.15			6.78			0.60
Total from Investment Operations		15.38			(0.07	)		6.49			0.51
Distributions from and/or in Excess of:
Net Realized Gain		(2.31	)		(3.68	)		(6.92	)		—
Net Asset Value, End of Period	$	28.74		$	15.67		$	19.42		$	19.85
Total Return(3)		113.21	%		3.55	%		46.08	%		2.64	%(6)
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	33,781		$	6,518		$	536		$	10
Ratio of Expenses Before Expense Limitation		1.75	%		1.84	%		3.69	%		15.31	%(7)
Ratio of Expenses After Expense Limitation		1.74	%(4)		1.83	%(4)		1.89	%(4)		1.90	%(4)(7)
Ratio of Expenses After Expense Limitation Excluding Non-Operating Expenses		1.74	%(4)		1.83	%(4)		1.89	%(4)		1.90	%(4)(7)
Ratio of Net Investment Loss		(1.59	)%(4)		(1.32	)%(4)		(1.58	)%(4)		(1.34	)%(4)(7)
Ratio of Rebate from Morgan Stanley Affiliates		0.01	%		0.01	%		0.01	%		0.00	%(5)(7)
Portfolio Turnover Rate		65	%		116	%		86	%		59	%(6)

(1)  Commencement of Offering.

(2)  Per share amount is based on average shares outstanding.

(3)  Calculated based on the net asset value which does not reflect sales charges, if applicable, as of the last business day of the period.

(4)  The Ratio of Expenses After Expense Limitation and Ratio of Net Investment Loss reflect the rebate of certain Fund expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates."

(5)  Amount is less than 0.005%.

(6)  Not annualized.

(7)  Annualized.

The accompanying notes are an integral part of the financial statements.
16

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Discovery Portfolio

	Class IS
	Year Ended September 30,
Selected Per Share Data and Ratios	2020			2019			2018			2017			2016(1)
Net Asset Value, Beginning of Period	$	20.15		$	23.50		$	22.43		$	31.94		$	36.03
Income (Loss) from Investment Operations:
Net Investment Income (Loss)(2)		(0.12	)		(0.04	)		(0.06	)		0.04			0.07
Net Realized and Unrealized Gain		21.00			0.37			8.05			2.04			0.16
Total from Investment Operations		20.88			0.33			7.99			2.08			0.23
Distributions from and/or in Excess of:
Net Realized Gain		(2.31	)		(3.68	)		(6.92	)		(11.59	)		(4.32	)
Net Asset Value, End of Period	$	38.72		$	20.15		$	23.50		$	22.43		$	31.94
Total Return(3)		115.65	%		4.77	%		47.89	%		16.24	%		0.25	%
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	354,067		$	130,653		$	93,005		$	63,225		$	219,255
Ratio of Expenses Before Expense Limitation		0.64	%		0.64	%		0.66	%		0.65	%		0.62	%
Ratio of Expenses After Expense Limitation		0.63	%(4)		0.63	%(4)		0.65	%(4)		0.65	%(4)		0.61	%(4)
Ratio of Expenses After Expense Limitation Excluding Non-Operating Expenses		0.63	%(4)		0.63	%(4)		0.65	%(4)		0.65	%(4)		N/A
Ratio of Net Investment Income (Loss)		(0.44	)%(4)		(0.18	)%(4)		(0.30	)%(4)		0.18	%(4)		0.22	%(4)
Ratio of Rebate from Morgan Stanley Affiliates		0.01	%		0.01	%		0.01	%		0.01	%		0.00	%(5)
Portfolio Turnover Rate		65	%		116	%		86	%		59	%		23	%

(1)  Reflects prior period custodian out-of-pocket expenses that were reimbursed in September 2016. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class IS shares. The Ratio of Expenses After Expense Limitation would have been less than 0.005% higher and the Ratio of Net Investment Income would have been less than 0.005% lower had the custodian not reimbursed the Fund.

(2)  Per share amount is based on average shares outstanding.

(3)  Calculated based on the net asset value as of the last business day of the period.

(4)  The Ratio of Expenses After Expense Limitation and Ratio of Net Investment Income (Loss) reflect the rebate of certain Fund expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates."

(5)  Amount is less than 0.005%.

The accompanying notes are an integral part of the financial statements.
17

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements

Morgan Stanley Institutional Fund Trust ("Trust'') is registered under the Investment Company Act of 1940, as amended (the "Act''), as an open-end management investment company. The Trust is comprised of twelve separate, active funds (individually referred to as a "Fund," collectively as the "Funds"). The Trust applies investment company accounting and reporting guidance. All Funds are considered diversified for purposes of the Act.

The accompanying financial statements relate to the Discovery Portfolio. The Fund seeks long-term capital growth. The Fund offers five classes of shares — Class I, Class A, Class L, Class C and Class IS.

The Fund has suspended offering of Class L shares for sale to all investors. Class L shareholders of the Fund do not have the option of purchasing additional Class L shares. However, existing Class L shareholders may invest in additional Class L shares through reinvestment of dividends and distributions.

A. Significant Accounting Policies: The following significant accounting policies are in conformity with U.S. generally accepted accounting principles ("GAAP"). Such policies are consistently followed by the Trust in the preparation of its financial statements. GAAP may require management to make estimates and assumptions that affect the reported amounts and disclosures in the financial statements. Actual results may differ from those estimates.

1.  Security Valuation: (1) An equity portfolio security listed or traded on an exchange is valued at its latest reported sales price (or at the exchange official closing price if such exchange reports an official closing price), and if there were no sales on a given day and if there is no official exchange closing price for that day, the security is valued at the mean between the last reported bid and asked prices if such bid and asked prices are available on the relevant exchanges. If only bid prices are available then the latest bid price may be used. Listed equity securities not traded on the valuation date with no reported bid and asked prices available on the exchange are valued at the mean between the current bid and asked prices obtained from one or more reputable brokers or dealers. In cases where a security is traded on more than one exchange, the security is valued on the exchange designated as the primary market; (2) all other equity portfolio securities for which over-the-counter ("OTC") market quotations are readily available are valued at the latest reported sales price (or at the market official closing price if such market reports an official closing price), and if there was no trading in the security

on a given day and if there is no official closing price from relevant markets for that day, the security is valued at the mean between the last reported bid and asked prices if such bid and asked prices are available on the relevant markets. An unlisted equity security that does not trade on the valuation date and for which bid and asked prices from the relevant markets are unavailable is valued at the mean between the current bid and asked prices obtained from one or more reputable brokers or dealers; (3) listed options are valued at the last reported sales price on the exchange on which they are listed (or at the exchange official closing price if such exchange reports an official closing price). If an official closing price or last reported sales price is unavailable, the listed option should be fair valued at the mean between its latest bid and ask prices. Unlisted options are valued at the mean between their latest bid and ask prices from a broker/dealer or valued by a pricing service/vendor; (4) certain portfolio securities may be valued by an outside pricing service/vendor approved by the Trust's Board of Trustees (the "Trustees"). The pricing service/vendor may employ a pricing model that takes into account, among other things, bids, yield spreads and/or other market data and specific security characteristics. Alternatively, if a valuation is not available from an outside pricing service/vendor, and the security trades on an exchange, the security may be valued at its latest reported sale price (or at the exchange official closing price if such exchange reports an official closing price), prior to the time when assets are valued. If there are no sales on a given day and if there is no official exchange closing price for that day, the security is valued at the mean between the last reported bid and asked prices if such bid and asked prices are available in the relevant exchanges. If only bid prices are available then the latest bid price may be used. If Morgan Stanley Investment Management Inc. (the "Adviser"), a wholly-owned subsidiary of Morgan Stanley, determines that the price provided by the outside pricing service/vendor or exchange does not reflect the security's fair value or is unable to provide a price, prices from brokers or dealers may also be utilized. In these circumstances, the value of the security will be the mean of bid and asked prices obtained from brokers or dealers; (5) when market quotations are not readily available, including circumstances under which the Adviser determines that the closing price, last sale price or the mean between the last reported bid and asked prices are not reflective of a security's market value, portfolio securities are valued at

18

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

their fair value as determined in good faith under procedures established by and under the general supervision of the Trustees. Occasionally, developments affecting the closing prices of securities and other assets may occur between the times at which valuations of such securities are determined (that is, close of the foreign market on which the securities trade) and the close of business of the New York Stock Exchange ("NYSE"). If developments occur during such periods that are expected to materially affect the value of such securities, such valuations may be adjusted to reflect the estimated fair value of such securities as of the close of the NYSE, as determined in good faith by the Trustees or by the Adviser using a pricing service and/or procedures approved by the Trustees; (6) quotations of foreign portfolio securities, other assets and liabilities and forward contracts stated in foreign currency are translated into U.S. dollar equivalents at the prevailing market rates prior to the close of the NYSE; and (7) investments in mutual funds, including the Morgan Stanley Institutional Liquidity Funds, are valued at the net asset value ("NAV") as of the close of each business day.

The Trustees have responsibility for determining in good faith the fair value of the investments, and the Trustees may appoint others, such as the Trust's Adviser or a valuation committee, to assist the Trustees in determining fair value and to make the actual calculations pursuant to the fair valuation methodologies previously approved by the Trustees. Under procedures approved by the Trustees, the Trust's Adviser has formed a Valuation Committee whose members are approved by the Trustees. The Valuation Committee provides administration and oversight of the Trust's valuation policies and procedures, which are reviewed at least annually by the Trustees. These procedures allow the Trust to utilize independent pricing services, quotations from securities and financial instrument dealers and other market sources to determine fair value.

2.  Fair Value Measurement: FASB Accounting Standards Codification^TM ("ASC") 820, "Fair Value Measurement" ("ASC 820"), defines fair value as the value that the Fund would receive to sell an investment or pay to transfer a liability in a timely transaction with an independent

buyer in the principal market, or in the absence of a principal market, the most advantageous market for the investment or liability. ASC 820 establishes a three-tier hierarchy to distinguish between (1) inputs that reflect the assumptions market participants would use in valuing an asset or liability developed based on market data obtained from sources independent of the reporting entity (observable inputs) and (2) inputs that reflect the reporting entity's own assumptions about the assumptions market participants would use in valuing an asset or liability developed based on the best information available in the circumstances (unobservable inputs) and to establish classification of fair value measurements for disclosure purposes. Various inputs are used in determining the value of the Fund's investments. The inputs are summarized in the three broad levels listed below:

•  Level 1 – unadjusted quoted prices in active markets for identical investments

•  Level 2 – other significant observable inputs (including quoted prices for similar investments, interest rates, prepayment speeds, credit risk, etc.)

•  Level 3 – significant unobservable inputs including the Fund's own assumptions in determining the fair value of investments. Factors considered in making this determination may include, but are not limited to, information obtained by contacting the issuer, analysts, or the appropriate stock exchange (for exchange-traded securities), analysis of the issuer's financial statements or other available documents and, if necessary, available information concerning other securities in similar circumstances.

The inputs or methodology used for valuing securities are not necessarily an indication of the risk associated with investing in those securities and the determination of the significance of a particular input to the fair value measurement in its entirety requires judgment and considers factors specific to each security.

19

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

The following is a summary of the inputs used to value the Fund's investments as of September 30, 2020:

Investment Type	Level 1 Unadjusted quoted prices (000)		Level 2 Other significant observable inputs (000)		Level 3 Significant unobservable inputs (000)		Total (000)
Assets:
Common Stocks
Biotechnology	$	41,391	$	—	$	—	$	41,391
Electronic Equipment, Instruments & Components		23,550		—		—		23,550
Entertainment		160,882		—		—		160,882
Health Care Equipment & Supplies		125,503		—		—		125,503
Health Care Providers & Services		121,645		—		—		121,645
Health Care Technology		198,875		—		3,980		202,855
Information Technology Services		699,925		49,355		—		749,280
Interactive Media & Services		323,774		—		—		323,774
Internet & Direct Marketing Retail		231,089		—		—		231,089
Leisure Products		88,726		—		—		88,726
Life Sciences Tools & Services		161,397		—		—		161,397
Metals & Mining		4,093		—		—		4,093
Oil, Gas & Consumable Fuels		3,830		—		—		3,830
Pharmaceuticals		38,137		—		—		38,137
Semiconductors & Semiconductor Equipment		21,336		—		—		21,336
Software		531,479		—		—		531,479
Specialty Retail		136,800		—		—		136,800
Total Common Stocks		2,912,432		49,355		3,980		2,965,767

Investment Type	Level 1 Unadjusted quoted prices (000)		Level 2 Other significant observable inputs (000)		Level 3 Significant unobservable inputs (000)		Total (000)
Preferred Stocks
Internet & Direct Marketing Retail	$	2,774	$	—	$	—	$	2,774
Call Options Purchased		—		3,218		—		3,218
Short-Term Investments
Investment Company		89,721		—		—		89,721
Repurchase Agreements		—		2,060		—		2,060
Total Short-Term Investments		89,721		2,060		—		91,781
Total Assets	$	3,004,927	$	54,633	$	3,980	$	3,063,540

Transfers between investment levels may occur as the markets fluctuate and/or the availability of data used in an investment's valuation changes.

Following is a reconciliation of investments in which significant unobservable inputs (Level 3) were used in determining fair value:

	Common Stock (000)
Beginning Balance	$	2,832
Purchases		—
Sales		—
Amortization of discount		—
Transfers in		—
Transfers out		—
Corporate actions		—
Change in unrealized appreciation (depreciation)		1,148
Realized gains (losses)		—
Ending Balance	$	3,980
Net change in unrealized appreciation (depreciation) from investments still held as of September 30, 2020	$	1,148

The following table presents additional information about valuation techniques and inputs used for investments that are measured at fair value and categorized within Level 3 as of September 30, 2020:

	Fair Value at September 30, 2020 (000)		Valuation Technique	Unobservable Input	Amount*			Impact to Valuation from an Increase in Input**
Common Stock	$	3,980	Discounted Cash Flow	Weighted Average Cost of Capital		12.5	%	Decrease
				Perpetual Growth Rate		3.5	%	Increase
			Market Comparable Companies	Enterprise Value/ Revenue		1.1x		Increase
				Discount for Lack of Marketability		12.0	%	Decrease

*  Amount is indicative of the weighted average.

**  Represents the expected directional change in the fair value of the Level 3 investments that would result from an increase in the corresponding input. A decrease to the unobservable input would have the opposite effect. Significant changes in these inputs could result in significantly higher or lower fair value measurements.

20

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

3.  Repurchase Agreements: The Fund may enter into repurchase agreements under which the Fund lends cash and takes possession of securities with an agreement that the counterparty will repurchase such securities. In connection with transactions in repurchase agreements, a bank as custodian for the Fund takes possession of the underlying securities which are held as collateral, with a market value at least equal to the amount of the repurchase transaction, including principal and accrued interest. To the extent that any repurchase transaction exceeds one business day, the value of the collateral is marked-to-market on a daily basis to determine that the value of the collateral does not decrease below the repurchase price plus accrued interest as earned. If such a decrease occurs, additional collateral will be requested and, when received, will be added to the account to maintain full collateralization. In the event of default on the obligation to repurchase, the Fund has the right to liquidate the collateral and apply the proceeds in satisfaction of the obligation. In the event of default or bankruptcy by the counterparty to the agreement, realization of the collateral proceeds may be subject to cost and delays. The Fund, along with other affiliated investment companies, may utilize a joint trading account for the purpose of entering into repurchase agreements.

4.  Foreign Currency Translation and Foreign Investments: The books and records of the Fund are maintained in U.S. dollars. Foreign currency amounts are translated into U.S. dollars as follows:

–  investments, other assets and liabilities at the prevailing rate of exchange on the valuation date;

–  investment transactions and investment income at the prevailing rates of exchange on the dates of such transactions.

Although the net assets of the Fund are presented at the foreign exchange rates and market values at the close of the period, the Fund does not isolate that portion of the results of operations arising as a result of changes in the foreign exchange rates from the fluctuations arising from changes in the market prices of securities held at period end. Similarly, the Fund does not isolate the effect of changes in foreign exchange rates from the fluctuations arising from changes in the market prices of securities sold during the period. Accordingly, realized and unrealized foreign currency gains (losses) on invest-

ments in securities are included in the reported net realized and unrealized gains (losses) on investment transactions and balances. However, pursuant to U.S. federal income tax regulations, gains and losses from certain foreign currency transactions and the foreign currency portion of gains and losses realized on sales and maturities of foreign denominated debt securities are treated as ordinary income for U.S. federal income tax purposes.

Net realized gains (losses) on foreign currency transactions represent net foreign exchange gains (losses) from foreign currency forward exchange contracts, disposition of foreign currencies, currency gains (losses) realized between the trade and settlement dates on securities transactions, and the difference between the amount of investment income and foreign withholding taxes recorded on the Fund's books and the U.S. dollar equivalent amounts actually received or paid. The change in unrealized currency gains (losses) on foreign currency transactions for the period is reflected in the Statement of Operations.

Foreign security and currency transactions may involve certain considerations and risks not typically associated with those of U.S. dollar denominated transactions as a result of, among other factors, fluctuations of exchange rates in relation to the U.S. dollar, the possibility of lower levels of governmental supervision and regulation of foreign securities markets and the possibility of political or economic instability.

Governmental approval for foreign investments may be required in advance of making an investment under certain circumstances in some countries, and the extent of foreign investments in domestic companies may be subject to limitation in other countries. Foreign ownership limitations also may be imposed by the charters of individual companies to prevent, among other concerns, violations of foreign investment limitations. As a result, an additional class of shares (identified as "Foreign" in the Portfolio of Investments) may be created and offered for investment. The "local" and "foreign shares" market values may differ. In the absence of trading of the foreign shares in such markets, the Fund values the foreign shares at the closing exchange price of the local shares.

5.  Derivatives: The Fund may, but is not required to, use derivative instruments for a variety of purposes, including hedging, risk management, portfolio management or to

21

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

earn income. Derivatives are financial instruments whose value is based, in part, on the value of an underlying asset, interest rate, index or financial instrument. Prevailing interest rates and volatility levels, among other things, also affect the value of derivative instruments. A derivative instrument often has risks similar to its underlying asset and may have additional risks, including imperfect correlation between the value of the derivative and the underlying asset, risks of default by the counterparty to certain transactions, magnification of losses incurred due to changes in the market value of the securities, instruments, indices or interest rates to which the derivative instrument relates, risks that the transactions may not be liquid and risks arising from margin requirements. The use of derivatives involves risks that are different from, and possibly greater than, the risks associated with other portfolio investments. Derivatives may involve the use of highly specialized instruments that require investment techniques and risk analyses different from those associated with other portfolio investments. All of the Fund's holdings, including derivative instruments, are marked-to-market each day with the change in value reflected in unrealized appreciation (depreciation). Upon disposition, a realized gain or loss is recognized.

Certain derivative transactions may give rise to a form of leverage. Leverage magnifies the potential for gain and the risk of loss. Leverage associated with derivative transactions may cause the Fund to liquidate portfolio positions when it may not be advantageous to do so to satisfy its obligations or to meet earmarking or segregation requirements, pursuant to applicable Securities and Exchange Commission ("SEC") rules and regulations, or may cause the Fund to be more volatile than if the Fund had not been leveraged. Although the Adviser seeks to use derivatives to further the Fund's investment objectives, there is no assurance that the use of derivatives will achieve this result.

Following is a description of the derivative instruments and techniques that the Fund used during the period and their associated risks:

Options: With respect to options, the Fund is subject to equity risk, interest rate risk and foreign currency exchange risk in the normal course of pursuing its investment objectives. If the Fund buys an option, it

buys a legal contract giving it the right to buy or sell a specific amount of the underlying instrument or foreign currency, or futures contract on the underlying instrument or foreign currency, at an agreed-upon price during a period of time or on a specified date typically in exchange for a premium paid by the Fund. The Fund may purchase and/or sell put and call options. Purchasing call options tends to increase the Fund's exposure to the underlying (or similar) instrument. Purchasing put options tends to decrease the Fund's exposure to the underlying (or similar) instrument. When entering into purchased option contracts, the Fund bears the risk of interest or exchange rates or securities prices moving unexpectedly, in which case, the Fund may not achieve the anticipated benefits of the purchased option contracts; however the risk of loss is limited to the premium paid. Purchased options are reported as part of "Total Investments in Securities" in the Statement of Assets and Liabilities. Premium paid for purchasing options which expired are treated as realized losses. If the Fund sells an option, it sells to another party the right to buy from or sell to the Fund a specific amount of the underlying instrument or foreign currency, or futures contract on the underlying instrument or foreign currency, at an agreed-upon price during a period of time or on a specified date typically in exchange for a premium received by the Fund. When options are purchased OTC, the Fund bears the risk that the counterparty that wrote the option will be unable or unwilling to perform its obligations under the option contract. Options may also be illiquid and the Fund may have difficulty closing out its position. A decision as to whether, when and how to use options involves the exercise of skill and judgment and even a well-conceived option transaction may be unsuccessful because of market behavior or unexpected events. The prices of options can be highly volatile and the use of options can lower total returns.

FASB ASC 815, "Derivatives and Hedging" ("ASC 815"), is intended to improve financial reporting about derivative instruments by requiring enhanced disclosures to enable investors to better understand how and why the Fund uses derivative instruments, how these derivative instruments are accounted for and their effects on the Fund's financial position and results of operations.

22

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

The following table sets forth the fair value of the Fund's derivative contracts by primary risk exposure as of September 30, 2020:

	Asset Derivatives Statement of Assets and Liabilities Location	Primary Risk Exposure	Value (000)
Purchased Options	Investments, at Value (Purchased Options)	Currency Risk	$	3,218	(a)

(a) Amounts are included in Investments in Securities in the Statement of Assets and Liabilities.

The following tables set forth by primary risk exposure the Fund's realized gains (losses) and change in unrealized appreciation (depreciation) by type of derivative contract for the year ended September 30, 2020 in accordance with ASC 815:

Realized Gain (Loss)
Primary Risk Exposure	Derivative Type	Value (000)
Currency Risk	Investments (Purchased Options)		$(3,178)(b)

(b) Amounts are included in Investments Sold in the Statement of Operations.

Change in Unrealized Appreciation (Depreciation)
Primary Risk Exposure	Derivative Type	Value (000)
Currency Risk	Investments (Purchased Options)		$(2,754)(c)

(c) Amounts are included in Investments in the Statement of Operations.

At September 30, 2020, the Fund's derivative assets and liabilities are as follows:

Gross Amounts of Assets and Liabilities Presented in the Statement of Assets and Liabilities
Derivatives	Assets(d) (000)			Liabilities(d) (000)
Purchased Options	$	3,218	(a)	$	—

(a) Amounts are included in Investments in Securities in the Statement of Assets and Liabilities.

(d)  Absent an event of default or early termination, OTC derivative assets and liabilities are presented gross and not offset in the Statement of Assets and Liabilities.

The Fund typically enters into International Swaps and Derivatives Association, Inc. Master Agreements ("ISDA Master Agreements") or similar master agreements (collectively, "Master Agreements") with its contract counterparties for certain OTC derivatives in order to, among other things, reduce its credit risk to counterparties. ISDA Master Agreements include provisions for general obligations, representations, collateral and events of default or termination. Under an ISDA Master Agreement, the Fund typically may offset with the counterparty certain OTC derivative financial instruments' payables and/or receivables with collateral held

and/or posted and create one single net payment (close-out netting) in the event of default, termination and/or potential deterioration in the credit quality of the counterparty. Various Master Agreements govern the terms of certain transactions with counterparties, including transactions such as swap, forward, repurchase and reverse repurchase agreements. These Master Agreements typically attempt to reduce the counterparty risk associated with such transactions by specifying credit protection mechanisms and providing standardization that improves legal certainty. Cross-termination provisions under Master Agreements typically provide that a default in connection with one transaction between the Fund and a counterparty gives the non-defaulting party the right to terminate any other transactions in place with the defaulting party to create one single net payment due to/due from the defaulting party and may be a feature in certain Master Agreements. In the event the Fund exercises its right to terminate a Master Agreement after a counterparty experiences a termination event as defined in the Master Agreement, the return of collateral with market value in excess of the Fund's net liability may be delayed or denied.

The following table presents derivative financial instruments that are subject to enforceable netting arrangements as of September 30, 2020:

Gross Amounts Not Offset in the Statement of Assets and Liabilities
Counterparty	Gross Asset Derivatives Presented in the Statement of Assets and Liabilities(a) (000)		Financial Instrument (000)		Collateral Received(e) (000)			Net Amount (not less than $0) (000)
BNP Paribas	$	1,654	$	—	$	(1,654	)	$	0
Royal Bank of Scotland		1,564		—		(1,564	)		0
Total	$	3,218	$	—	$	(3,218	)	$	0

(a) Amounts are included in Investments in Securities in the Statement of Assets and Liabilities.

(e) In some instances, the actual collateral received may be more than the amount shown here due to overcollateralization.

For the year ended September 30, 2020, the approximate average monthly amount outstanding for each derivative type is as follows:

Options Purchased:
Average monthly notional amount	710,671,000

6.  Securities Lending: The Fund lends securities to qualified financial institutions, such as broker-dealers, to earn additional income. Any increase or decrease in the fair

23

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

value of the securities loaned that might occur and any interest earned or dividends declared on those securities during the term of the loan would remain in the Fund. The Fund would receive cash or securities as collateral in an amount equal to or exceeding 100% of the current fair value of the loaned securities. The collateral is marked-to-market daily by State Street Bank and Trust Company ("State Street"), the securities lending agent, to ensure that a minimum of 100% collateral coverage is maintained.

Based on pre-established guidelines, the securities lending agent invests any cash collateral that is received in an affiliated money market portfolio and repurchase agreements. Securities lending income is generated from the earnings on the invested collateral and borrowing fees, less any rebates owed to the borrowers and compensation to the lending agent, and is recorded as "Income from Securities Loaned — Net" in the Fund's Statement of Operations. Risks in securities lending transactions are that a borrower may not provide additional collateral when required or return the securities when due, and that the value of the short-term investments will be less than the amount of cash collateral plus any rebate that is required to be returned to the borrower.

The Fund has the right under the securities lending agreement to recover the securities from the borrower on demand.

The following table presents financial instruments that are subject to enforceable netting arrangements as of September 30, 2020:

Gross Amounts Not Offset in the Statement of Assets and Liabilities
Gross Asset Amounts Presented in the Statement of Assets and Liabilities (000)			Financial Instrument (000)		Collateral Received (000)			Net Amount (not less than $0) (000)
$	10,527	(f)	$	—	$	(10,527	)(g)(h)	$	0

(f)  Represents market value of loaned securities at year end.

(g)  The Fund received cash collateral of approximately $11,093,000, which was subsequently invested in Repurchase Agreements and Morgan Stanley Institutional Liquidity Funds as reported in the Portfolio of Investments.

(h)  The actual collateral received is greater than the amount shown here due to overcollateralization.

FASB ASC 860, "Transfers & Servicing: Repurchase-to-Maturity Transactions, Repurchase Financings, and Disclosures", is intended to provide increased transparency about the types of collateral pledged in securities lending

transactions and other similar transactions that are accounted for as secured borrowing.

The following table displays a breakdown of transactions accounted for as secured borrowings, the gross obligations by class of collateral pledged and the remaining contractual maturity of those transactions as of September 30, 2020:

Remaining Contractual Maturity of the Agreements
	Overnight and Continuous (000)		<30 days (000)		Between 30 & 90 days (000)		>90 days (000)		Total (000)
Securities Lending Transactions
Common Stocks	$	11,087	$	—	$	—	$	—	$	11,087
Preferred Stocks		6		—		—		—		6
Total	$	11,093	$	—	$	—	$	—	$	11,093
Total Borrowings	$	11,093	$	—	$	—	$	—	$	11,093
Gross amount of recognized liabilities for securities lending transactions									$	11,093

7.  Restricted Securities: The Fund invests in unregistered or otherwise restricted securities. The term "restricted securities" refers to securities that are unregistered or are held by control persons of the issuer and securities that are subject to contractual restrictions on their resale. As a result, restricted securities may be more difficult to value and the Fund may have difficulty disposing of such assets either in a timely manner or for a reasonable price. In order to dispose of an unregistered security, the Fund, where it has contractual rights to do so, may have to cause such security to be registered. A considerable period may elapse between the time the decision is made to sell the security and the time the security is registered so that the Fund can sell it. Contractual restrictions on the resale of securities vary in length and scope and are generally the result of a negotiation between the issuer and the acquirer of the securities. The Fund would, in either case, bear market risks during that period. Restricted securities are identified in the Portfolio of Investments.

8.  Indemnifications: The Trust enters into contracts that contain a variety of indemnifications. The Trust's maximum exposure under these arrangements is unknown. However, the Trust has not had prior claims or losses pursuant to these contracts and expects the risk of loss to be remote.

24

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

9.  Dividends and Distributions to Shareholders: Dividends and distributions to shareholders are recorded on the ex-dividend date. Dividends from net investment income, if any, are declared and paid annually. Net realized capital gains, if any, are distributed at least annually.

10.  Security Transactions, Income and Expenses: Security transactions are accounted for on the trade date (date the order to buy or sell is executed). Realized gains and losses on the sale of investment securities are determined on the specific identified cost method. Dividend income and other distributions are recorded on the ex-dividend date (except for certain foreign dividends which may be recorded as soon as the Fund is informed of such dividends) net of applicable withholding taxes. Interest income is recognized on the accrual basis except where collection is in doubt. Discounts are accreted and premiums are amortized over the life of the respective securities. Most expenses of the Trust can be directly attributed to a particular Fund. Expenses which cannot be directly attributed are apportioned among the Funds based upon relative net assets or other appropriate methods. Income, expenses (other than class specific expenses — distribution and shareholder services, transfer agency and sub transfer agency fees) and realized and unrealized gains or losses are allocated to each class of shares based upon their relative net assets.

B. Advisory Fees: The Adviser, a wholly-owned subsidiary of Morgan Stanley, provides the Fund with advisory services under the terms of an Investment Advisory Agreement, paid quarterly, at an annual rate of 0.50% of the average daily net assets of the Fund.

The Adviser has agreed to reduce its advisory fee and/or reimburse the Fund so that total annual Fund operating expenses, excluding certain investment related expenses, taxes, interest and other extraordinary expenses (including litigation), will not exceed 0.80% for Class I shares, 1.15% for Class A shares, 1.65% for Class L shares, 1.90% for Class C shares and 0.73% for Class IS shares. The fee waivers and/or expense reimbursements will continue for at least one year from the date of the Fund's prospectus or until such time as the Trustees act to discontinue all or a portion of such waivers and/or reimbursements when they deem such action is appropriate.

C. Administration Fees: The Adviser also serves as Administrator to the Trust and provides administrative services pursuant to an Administration Agreement for an annual fee,

accrued daily and paid monthly, of 0.08% of the Fund's average daily net assets. Under a Sub-Administration Agreement between the Administrator and State Street, State Street provides certain administrative services to the Trust. For such services, the Administrator pays State Street a portion of the fee the Administrator receives from the Fund.

D. Distribution and Shareholder Services Fees: Morgan Stanley Distribution, Inc. ("MSDI" or the "Distributor"), a wholly-owned subsidiary of the Adviser, and an indirect subsidiary of Morgan Stanley, serves as the Trust's Distributor of Fund shares pursuant to a Distribution Agreement. The Trust has adopted a Shareholder Services Plan with respect to Class A shares pursuant to Rule 12b-1 under the Act. Under the Shareholder Services Plan, the Fund pays the Distributor a shareholder services fee, accrued daily and paid monthly, at an annual rate of 0.25% of the Fund's average daily net assets attributable to Class A shares.

The Trust has adopted a Distribution and Shareholder Services Plan with respect to Class L shares pursuant to Rule 12b-1 under the Act. Under the Distribution and Shareholder Services Plan, the Fund pays the Distributor a distribution fee, accrued daily and paid monthly, at an annual rate of 0.50% and a shareholder services fee, accrued daily and paid monthly, at an annual rate of 0.25% of the Fund's average daily net assets attributable to Class L shares.

The Trust has adopted a Distribution and Shareholder Services Plan with respect to Class C shares pursuant to Rule 12b-1 under the Act. Under the Distribution and Shareholder Services Plan, the Fund pays the Distributor a distribution fee, accrued daily and paid monthly, at an annual rate of 0.75% and a shareholder services fee, accrued daily and paid monthly, at an annual rate of 0.25% of the Fund's average daily net assets attributable to Class C shares.

The distribution and shareholder services fees are used to support the expenses associated with servicing and maintaining accounts. The Distributor may compensate other parties for providing shareholder support services to investors who purchase Class A, Class L and Class C shares.

E. Dividend Disbursing and Transfer Agent: The Trust's dividend disbursing and transfer agent is DST Asset Manager Solutions, Inc. ("DST"). Pursuant to a Transfer Agency Agreement, the Trust pays DST a fee based on the number of classes, accounts and transactions relating to the Funds of the Trust.

25

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

F. Custodian Fees: State Street (the "Custodian") also serves as Custodian for the Trust in accordance with a Custodian Agreement. The Custodian holds cash, securities and other assets of the Trust as required by the Act. Custody fees are payable monthly based on assets held in custody, investment purchases and sales activity and account maintenance fees, plus reimbursement for certain out-of-pocket expenses.

G. Security Transactions and Transactions with Affiliates: For the year ended September 30, 2020, purchases and sales of investment securities for the Fund, other than long-term U.S. Government securities and short-term investments were approximately $1,768,319,000 and $900,098,000, respectively. There were no purchases and sales of long-term U.S. Government securities for the year ended September 30, 2020.

The Fund invests in the Institutional Class of the Morgan Stanley Institutional Liquidity Funds — Treasury Securities Portfolio (the "Liquidity Funds"), an open-end management investment company managed by the Adviser, both directly and as a portion of the securities held as collateral on loaned securities. Advisory fees paid by the Fund are reduced by an amount equal to its pro-rata share of the advisory and administration fees paid by the Fund due to its investment in the Liquidity Funds. For the year ended September 30, 2020, advisory fees paid were reduced by approximately $147,000 relating to the Fund's investment in the Liquidity Funds.

A summary of the Fund's transactions in shares of affiliated investments during the year ended September 30, 2020 is as follows:

Affiliated Investment Company	Value September 30, 2019 (000)		Purchases at Cost (000)		Proceeds from Sales (000)		Dividend Income (000)
Liquidity Funds	$	66,220	$	1,261,759	$	1,238,258	$	192

Affiliated Investment Company (cont'd)	Realized Gain (Loss) (000)		Change in Unrealized Appreciation (Depreciation) (000)		Value September 30, 2020 (000)
Liquidity Funds	$	—	$	—	$	89,721

The Fund is permitted to purchase and sell securities ("cross-trade") from and to other Morgan Stanley funds as well as other funds and client accounts for which the Adviser or an affiliate of the Adviser serves as investment adviser, pursuant to procedures approved by the Trustees in compliance with

Rule 17a-7 under the Act (the "Rule"). Each cross-trade is executed at the current market price in compliance with provisions of the Rule. For the year ended September 30, 2020, the Fund engaged in cross-trade purchases of approximately $1,439,000.

The Fund has an unfunded Deferred Compensation Plan (the "Compensation Plan"), which allows each independent Trustee to defer payment of all, or a portion, of the fees he or she receives for serving on the Board of Trustees. Each eligible Trustee generally may elect to have the deferred amounts credited with a return equal to the total return on one or more of the Morgan Stanley funds that are offered as investment options under the Compensation Plan. Appreciation/depreciation and distributions received from these investments are recorded with an offsetting increase/decrease in the deferred compensation obligation and do not affect the NAV of the Fund.

H. Federal Income Taxes: It is the Fund's intention to continue to qualify as a regulated investment company and distribute all of its taxable and tax-exempt income. Accordingly, no provision for federal income taxes is required in the financial statements.

The Fund may be subject to taxes imposed by countries in which it invests. Such taxes are generally based on income and/or capital gains earned or repatriated. Taxes are accrued based on net investment income, net realized gains and net unrealized appreciation as such income and/or gains are earned. Taxes may also be based on transactions in foreign currency and are accrued based on the value of investments denominated in such currency.

FASB ASC 740-10, "Income Taxes — Overall", sets forth a minimum threshold for financial statement recognition of the benefit of a tax position taken or expected to be taken in a tax return. Management has concluded there are no significant uncertain tax positions that would require recognition in the financial statements. If applicable, the Fund recognizes interest accrued related to unrecognized tax benefits in "Interest Expense" and penalties in "Other Expenses" in the Statement of Operations. The Fund files tax returns with the U.S. Internal Revenue Service, New York and various states. Generally, each of the tax years in the four-year period ended September 30, 2020 remains subject to examination by taxing authorities.

The tax character of distributions paid may differ from the character of distributions shown for GAAP purposes due to

26

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

short-term capital gains being treated as ordinary income for tax purposes. The tax character of distributions paid during fiscal years 2020 and 2019 was as follows:

2020 Distributions Paid From:				2019 Distributions Paid From:
Ordinary Income (000)		Long-Term Capital Gain (000)		Ordinary Income (000)		Long-Term Capital Gain (000)
$	21,323	$	80,708	$	10,731	$	110,644

The amount and character of income and gains to be distributed are determined in accordance with income tax regulations which may differ from GAAP. These book/tax differences are either considered temporary or permanent in nature.

Temporary differences are attributable to differing book and tax treatments for the timing of the recognition of gains (losses) on certain investment transactions and the timing of the deductibility of certain expenses.

Permanent differences, due to tax adjustments related to real estate investment trusts sold by the Fund, resulted in the following reclassifications among the components of net assets at September 30, 2020:

Total Distributable Earnings (000)		Paid-in- Capital (000)
$	150	$	(150	)

At September 30, 2020, the components of distributable earnings for the Fund on a tax basis were as follows:

Undistributed Ordinary Income (000)		Undistributed Long-Term Capital Gain (000)
$	56,162	$	192,756

I. Credit Facility: The Trust and other Morgan Stanley funds participated in a $300,000,000 committed, unsecured revolving line of credit facility (the "Facility") with State Street. This Facility is to be used for temporary emergency purposes or funding of shareholder redemption requests. The interest rate on borrowings is based on the federal funds rate or 1 month LIBOR rate plus a spread. The Facility also has a commitment fee of 0.25% per annum based on the unused portion of the Facility. During the year ended September 30, 2020, the Fund did not have any borrowings under the Facility.

J. Other: At September 30, 2020, the Fund had record owners of 10% or greater. Investment activities of these sharehold-

ers could have a material impact on the Fund. The aggregate percentage of such owners was 40.1%.

K. Market Risk: Certain impacts to public health conditions particular to the coronavirus (COVID-19) outbreak could impact the operations and financial performance of certain of the Fund's investments. The extent of the impact to the financial performance of the Fund's investments will depend on future developments, including (i) the duration and spread of the outbreak, (ii) the restrictions and advisories, (iii) the effects on the financial markets, and (iv) the effects on the economy overall, all of which are highly uncertain and cannot be predicted. If the financial performance of the Fund's investments is impacted because of these factors for an extended period, the Fund's investment results may be adversely affected.

27

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Report of Independent Registered Public Accounting Firm

To the Shareholders and Board of Trustees of
Morgan Stanley Institutional Fund Trust —
Discovery Portfolio

Opinion on the Financial Statements

We have audited the accompanying statement of assets and liabilities of Discovery Portfolio (the "Fund") (one of the funds constituting Morgan Stanley Institutional Fund Trust (the "Trust")), including the portfolio of investments, as of September 30, 2020, and the related statement of operations for the year then ended, the statements of changes in net assets for each of the two years in the period then ended, the financial highlights for each of the five years in the period then ended and the related notes (collectively referred to as the "financial statements"). In our opinion, the financial statements present fairly, in all material respects, the financial position of the Fund (one of the funds constituting Morgan Stanley Institutional Fund Trust) at September 30, 2020, the results of its operations for the year then ended, the changes in its net assets for each of the two years in the period then ended and its financial highlights for each of the five years in the period then ended, in conformity with U.S. generally accepted accounting principles.

Basis for Opinion

These financial statements are the responsibility of the Trust's management. Our responsibility is to express an opinion on the Fund's financial statements based on our audits. We are a public accounting firm registered with the Public Company Accounting Oversight Board (United States) ("PCAOB") and are required to be independent with respect to the Trust in accordance with the U.S. federal securities law and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB.

We conducted our audits in accordance with the standards of the PCAOB. Those standards require that we plan and perform the audit to obtain reasonable assurance about whether the financial statements are free of material misstatement, whether due to error or fraud. The Trust is not required to have, nor were we engaged to perform, an audit of the Trust's internal control over financial reporting. As part of our audits we are required to obtain an understanding of internal control over financial reporting but not for the purpose of expressing an opinion on the effectiveness of the Trust's internal control over financial reporting. Accordingly, we express no such opinion.

Our audits included performing procedures to assess the risks of material misstatement of the financial statements, whether due to error or fraud, and performing procedures that respond to those risks. Such procedures included examining, on a test basis, evidence regarding the amounts and disclosures in the financial statements. Our procedures included confirmation of securities owned as of September 30, 2020 by correspondence with the custodian and brokers or by other appropriate auditing procedures where replies from brokers were not received. Our audits also included evaluating the accounting principles used and significant estimates made by management, as well as evaluating the overall presentation of the financial statements. We believe that our audits provide a reasonable basis for our opinion.

We have served as the auditor of one or more Morgan Stanley investment companies since 2000.
Boston, Massachusetts
November 24, 2020

28

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Advisory Agreement Approval (unaudited)

Nature, Extent and Quality of Services

The Board reviewed and considered the nature and extent of the investment advisory services provided by the Adviser under the advisory agreement, including portfolio management, investment research and equity and fixed income securities trading. The Board also reviewed and considered the nature and extent of the non-advisory, administrative services provided by the Administrator under the administration agreement, including accounting, operations, clerical, bookkeeping, compliance, business management and planning, legal services and the provision of supplies, office space and utilities at the Adviser's expense. The Board also considered the Adviser's investment in personnel and infrastructure that benefits the Fund. (The Adviser and Administrator together are referred to as the "Adviser" and the advisory and administration agreements together are referred to as the "Management Agreement.") The Board also considered that the Adviser serves a variety of other investment advisory clients and has experience overseeing service providers. The Board also compared the nature of the services provided by the Adviser with similar services provided by non-affiliated advisers as prepared by Broadridge Financial Solutions, Inc. ("Broadridge").

The Board reviewed and considered the qualifications of the portfolio managers, the senior administrative managers and other key personnel of the Adviser who provide the advisory and administrative services to the Fund. The Board determined that the Adviser's portfolio managers and key personnel are well qualified by education and/or training and experience to perform the services in an efficient and professional manner. The Board concluded that the nature and extent of the advisory and administrative services provided were necessary and appropriate for the conduct of the business and investment activities of the Fund and supported its decision to approve the Management Agreement.

Performance, Fees and Expenses of the Fund

The Board reviewed the performance, fees and expenses of the Fund compared to its peers, as prepared by Broadridge, and to appropriate benchmarks where applicable. The Board discussed with the Adviser the performance goals and the actual results achieved in managing the Fund. When considering a fund's performance, the Board and the Adviser place emphasis on trends and longer-term returns (focusing on one-year, three-year and five-year performance, as of December 31, 2019, or since inception, as applicable). When a fund underperforms its benchmark and/or its peer group average, the Board and the Adviser discuss the causes of such underperformance and, where necessary, they discuss specific changes to investment strategy or investment personnel. The Board noted that the Fund's performance was better than its peer group average for the one-, three-, and five-year periods. The Board discussed with the Adviser the level of the advisory and administration fees (together, the "management fee") for this Fund relative to comparable funds and/or other accounts advised by the Adviser and/or compared to its peers as prepared by Broadridge. In addition to the management fee, the Board also reviewed the Fund's total expense ratio. The Board noted that the Fund's management fee and total expense ratio were lower than its peer group averages. After discussion, the Board concluded that the Fund's performance, management fee and total expense ratio were competitive with its peer group averages.

Economies of Scale

The Board considered the size and growth prospects of the Fund and how that relates to the Fund's total expense ratio and particularly the Fund's management fee rate, which does not include breakpoints. In conjunction with its review of the Adviser's profitability, the Board discussed with the Adviser how a change in assets can affect the efficiency or effectiveness of managing the Fund and whether the management fee level is appropriate relative to current and projected asset levels and/or whether the management fee structure reflects economies of scale as asset levels change. The Board has determined that its review of the actual and/or potential economies of scale of the Fund supports its decision to approve the Management Agreement.

Profitability of the Adviser and Affiliates

The Board considered information concerning the costs incurred and profits realized by the Adviser and its affiliates during the last year from their relationship with the Fund and during the last two years from their relationship with the Morgan Stanley Fund Complex and reviewed with the Adviser the cost allocation methodology used to determine the profitability of the Adviser and affiliates. The Board has determined that its review of the analysis of the Adviser's expenses and profitability supports its decision to approve the Management Agreement.

29

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Advisory Agreement Approval (unaudited) (cont'd)

Other Benefits of the Relationship

The Board considered other direct and indirect benefits to the Adviser and/or its affiliates derived from their relationship with the Fund and other funds advised by the Adviser. These benefits may include, among other things, fees for trading, distribution and/or shareholder servicing and for transaction processing and reporting platforms used by securities lending agents, and research received by the Adviser generated from commission dollars spent on funds' portfolio trading. The Board reviewed with the Adviser these arrangements and the reasonableness of the Adviser's costs relative to the services performed. The Board has determined that its review of the other benefits received by the Adviser or its affiliates supports its decision to approve the Management Agreement.

Resources of the Adviser and Historical Relationship Between the Fund and the Adviser

The Board considered whether the Adviser is financially sound and has the resources necessary to perform its obligations under the Management Agreement. The Board also reviewed and considered the historical relationship between the Fund and the Adviser, including the organizational structure of the Adviser, the policies and procedures formulated and adopted by the Adviser for managing the Fund's operations and the Board's confidence in the competence and integrity of the senior managers and key personnel of the Adviser. The Board concluded that the Adviser has the financial resources necessary to fulfill its obligations under the Management Agreement and that it is beneficial for the Fund to continue its relationship with the Adviser.

Other Factors and Current Trends

The Board considered the controls and procedures adopted and implemented by the Adviser and monitored by the Fund's Chief Compliance Officer and concluded that the conduct of business by the Adviser indicates a good faith effort on its part to adhere to high ethical standards in the conduct of the Fund's business.

As part of the Board's review, the Board received information from management on the impact of COVID-19 on the firm generally and the Adviser and the Fund in particular including, among other information, the pandemic's current and expected impact on the Fund's performance and operations.

General Conclusion

After considering and weighing all of the above factors, with various written materials and verbal information presented by the Adviser, the Board concluded that it would be in the best interest of the Fund and its shareholders to approve renewal of the Management Agreement for another year. In reaching this conclusion the Board did not give particular weight to any single piece of information or factor referenced above. The Board considered these factors and information over the course of the year and in numerous meetings, some of which were in executive session with only the independent Board members and their counsel present. It is possible that individual Board members may have weighed these factors, and the information presented, differently in reaching their individual decisions to approve the Management Agreement.

30

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Liquidity Risk Management Program (unaudited)

In compliance with Rule 22e-4 under the Investment Company Act of 1940, as amended (the "Liquidity Rule"), the Fund has adopted and implemented a liquidity risk management program (the "Program"), which is reasonably designed to assess and manage the risk that the Fund could not meet requests to redeem shares issued by the Fund without significant dilution of remaining investors' interests in the Fund (i.e., liquidity risk). The Fund's Board of Trustees (the "Board") previously approved the designation of the Liquidity Risk Subcommittee (the "LRS") as Program administrator. The LRS is comprised of representatives from various divisions within Morgan Stanley Investment Management.

At a meeting held on April 22-23, 2020, the Board reviewed a written report prepared by the LRS that addressed the Program's operation and assessed its adequacy, and effectiveness of implementation for the period from December 1, 2018, through December 31, 2019, as required under the Liquidity Rule. The report concluded that the Program operated effectively and was adequately and effectively implemented in all material aspects, and that the relevant controls and safeguards were appropriately designed to enable the LRS to administer the Program in compliance with the Liquidity Rule.

In accordance with the Program, the LRS assessed each Fund's liquidity risk no less frequently than annually taking into consideration certain factors, as applicable, such as (i) investment strategy and liquidity of portfolio investments, (ii) short-term and long-term cash flow projections and (iii) holdings of cash and cash equivalents and borrowing arrangements and other funding sources. Certain factors are considered under both normal and reasonably foreseeable stressed conditions.

Each Fund portfolio investment is classified into one of four liquidity categories, which classification is assessed at least monthly by the LRS. The classification is based on a determination of the number of days it is reasonably expected to take to convert the investment into cash, or sell or dispose of the investment, in current market conditions without significantly changing the market value of the investment. Liquidity classification determinations take into account various market, trading and investment-specific considerations, as well as market depth, and in some cases utilize third-party vendor data.

The Liquidity Rule limits a fund's investments in illiquid investments to 15% of its net assets and requires funds that do not primarily hold assets that are highly liquid investments to determine and maintain a minimum percentage of the fund's net assets to be invested in highly liquid investments (highly liquid investment minimum or "HLIM"). The LRS believes that the Program includes provisions reasonably designed to review, monitor and comply with the 15% limit on illiquid investments and for determining, periodically reviewing and complying with the HLIM requirement, as applicable.

There can be no assurance that the Program will achieve its objectives under all circumstances in the future. Please refer to the Fund's prospectus for more information regarding the Fund's exposure to liquidity risk and other risks to which it may be subject.

31

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Federal Tax Notice (unaudited)

For federal income tax purposes, the following information is furnished with respect to the distributions paid by the Fund during its taxable year ended September 30, 2020. For corporate shareholders, 4.49% of the dividends qualified for the dividends received deduction.

The Fund designated and paid approximately $80,708,000 as a long-term capital gain distribution.

For federal income tax purposes, the following information is furnished with respect to the Fund's earnings for its taxable year ended September 30, 2020. When distributed, certain earnings may be subject to a maximum tax rate of 15% as provided for by the Jobs and Growth Tax Relief Reconciliation Act of 2003. The Fund designated up to a maximum of approximately $1,217,000 as taxable at this lower rate.

In January, the Fund provides tax information to shareholders for the preceding calendar year.

32

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Privacy Notice (unaudited)  April 2019

FACTS	WHAT DOES MSIM DO WITH YOUR PERSONAL INFORMATION?
Why?	Financial companies choose how they share your personal information. Federal law gives consumers the right to limit some but not all sharing. Federal law also requires us to tell you how we collect, share, and protect your personal information. Please read this notice carefully to understand what we do.
What?	The types of personal information we collect and share depend on the product or service you have with us. This information can include: n Social Security number and income n investment experience and risk tolerance n checking account number and wire transfer instructions
How?	All financial companies need to share customers' personal information to run their everyday business. In the section below, we list the reasons financial companies can share their customers' personal information; the reasons MSIM chooses to share; and whether you can limit this sharing.

Reasons we can share your personal information	Does MSIM share?	Can you limit this sharing?
For our everyday business purposes — such as to process your transactions, maintain your account(s), respond to court orders and legal investigations, or report to credit bureaus	Yes	No
For our marketing purposes — to offer our products and services to you	Yes	No
For joint marketing with other financial companies	No	We don't share
For our affiliates' everyday business purposes — information about your transactions and experiences	Yes	No
For our affiliates' everyday business purposes — information about your creditworthiness	No	We don't share
For our affiliates to market to you	No	We don't share
For non-affiliates to market to you	No	We don't share

Questions?Call toll-free (844) 312-6327 or email: imprivacyinquiries@morganstanley.com

33

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Privacy Notice (unaudited) (cont'd)  April 2019

Who we are

Who is providing this notice? Morgan Stanley Investment Management, Inc. and its affiliated registered investment advisers, registered broker-dealers, and registered and unregistered funds ("MSIM")

What we do

How does MSIM protect my personal information?	To protect your personal information from unauthorized access and use, we use security measures that comply with federal law. These measures include computer safeguards and secured files and buildings. We have policies governing the proper handling of customer information by personnel and requiring third parties that provide support to adhere to appropriate security standards with respect to such information.
How does MSIM collect my personal information?	We collect your personal information, for example, when you n open an account or make deposits or withdrawals from your account n buy securities from us or make a wire transfer n give us your contact information We also collect your personal information from others, such as credit bureaus, affiliates, or other companies.
Why can't I limit all sharing?	Federal law gives you the right to limit only n sharing for affiliates' everyday business purposes — information about your creditworthiness n affiliates from using your information to market to you n sharing for non-affiliates to market to you State laws and individual companies may give you additional rights to limit sharing. See below for more on your rights under state law.

Definitions

Affiliates	Companies related by common ownership or control. They can be financial and non-financial companies. n Our affiliates include companies with a Morgan Stanley name and financial companies such as Morgan Stanley Smith Barney LLC and Morgan Stanley & Co.
Non-affiliates	Companies not related by common ownership or control. They can be financial and non-financial companies. n MSIM does not share with non-affiliates so they can market to you.
Joint marketing	A formal agreement between non-affiliated financial companies that together market financial products or services to you. n MSIM doesn't jointly market

Other Important Information

Vermont: Except as permitted by law, we will not share personal information we collect about Vermont residents with Non-affiliates unless you provide us with your written consent to share such information.

California: Except as permitted by law, we will not share personal information we collect about California residents with Non-affiliates and we will limit sharing such personal information with our Affiliates to comply with California privacy laws that apply to us.

34

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited)

Independent Trustees:

Name, Address and Birth Year of Independent Trustee	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years and Other Relevant Professional Experience	Number of Funds in Fund Complex Overseen by Independent Trustee**		Other Directorships Held by Independent Trustee***
Frank L. Bowman c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1944	Trustee	Since August 2006	President, Strategic Decisions, LLC (consulting) (since February 2009); Director or Trustee of various Morgan Stanley Funds (since August 2006); Chairperson of the Compliance and Insurance Committee (since October 2015); formerly, Chairperson of the Insurance Sub-Committee of the Compliance and Insurance Committee (2007-2015); served as President and Chief Executive Officer of the Nuclear Energy Institute (policy organization) (February 2005-November 2008); retired as Admiral, U.S. Navy after serving over 38 years on active duty including 8 years as Director of the Naval Nuclear Propulsion Program in the Department of the Navy and the U.S. Department of Energy (1996-2004); served as Chief of Naval Personnel (July 1994-September 1996) and on the Joint Staff as Director of Political Military Affairs (June 1992-July 1994); knighted as Honorary Knight Commander of the Most Excellent Order of the British Empire; awarded the Officier de l'Orde National du Mérite by the French Government; elected to the National Academy of Engineering (2009).		86	Director of Naval and Nuclear Technologies LLP; Director Emeritus of the Armed Services YMCA; Member of the National Security Advisory Council of the Center for U.S. Global Engagement and a member of the CNA Military Advisory Board; Trustee of Fairhaven United Methodist Church; Member of the Board of Advisors of the Dolphin Scholarship Foundation; Director of other various non-profit organizations; Formerly, Director of BP p.l.c. (November 2010-May 2019).
Kathleen A. Dennis c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1953	Trustee	Since August 2006	President, Cedarwood Associates (mutual fund and investment management consulting) (since July 2006); Chairperson of the Liquidity and Alternatives Sub-Committee of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 2006); formerly, Senior Managing Director of Victory Capital Management (1993-2006).		86	Director of various non-profit organizations.
Nancy C. Everett c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1955	Trustee	Since January 2015	Chief Executive Officer, Virginia Commonwealth University Investment Company (since November 2015); Owner, OBIR, LLC (institutional investment management consulting) (since June 2014); formerly, Managing Director, BlackRock, Inc. (February 2011-December 2013); and Chief Executive Officer, General Motors Asset Management (a/k/a Promark Global Advisors, Inc.) (June 2005-May 2010).		87	Formerly, Member of Virginia Commonwealth University School of Business Foundation (2005-2016); Member of Virginia Commonwealth University Board of Visitors (2013-2015); Member of Committee on Directors for Emerging Markets Growth Fund, Inc. (2007-2010); Chairperson of Performance Equity Management, LLC (2006-2010); and Chairperson, GMAM Absolute Return Strategies Fund, LLC (2006-2010).

35

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Address and Birth Year of Independent Trustee	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years and Other Relevant Professional Experience	Number of Funds in Fund Complex Overseen by Independent Trustee**		Other Directorships Held by Independent Trustee***
Jakki L. Haussler c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1957	Trustee	Since January 2015	Chairman, Opus Capital Group (since January 1996); formerly, Chief Executive Officer, Opus Capital Group (1996-2019); Director, Capvest Venture Fund, LP (May 2000-December 2011); Partner, Adena Ventures, LP (July 1999-December 2010); Director, The Victory Funds (February 2005-July 2008).		87	Director of Service Corporation International and Member, Audit Committee and Investment Committee; Director of Cincinnati Bell Inc. and Member, Audit Committee and Governance and Nominating Committee; Director of Northern Kentucky University Foundation and Member, Investment Committee; Member of Chase College of Law Transactional Law Practice Center Board of Advisors; Director of Chase College of Law Board of Visitors; formerly, Member, University of Cincinnati Foundation Investment Committee; Member, Miami University Board of Visitors (2008-2011); Trustee of Victory Funds (2005-2008) and Chairman, Investment Committee (2007-2008); Member, Service Provider Committee (2005-2008) and Director of Best Transport (2006-2019).
Dr. Manuel H. Johnson c/o Johnson Smick International, Inc. 220 I Street, NE — Suite 200 Washington, D.C. 20002 Birth Year 1949	Trustee	Since July 1991	Senior Partner, Johnson Smick International, Inc. (consulting firm); Chairperson of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since July 1991); Co-Chairman and a founder of the Group of Seven Council (G7C) (international economic commission); formerly, Chairperson of the Audit Committee (July 1991-September 2006), Vice Chairman of the Board of Governors of the Federal Reserve System and Assistant Secretary of the U.S. Treasury.		86	Director of NVR, Inc. (home construction).
Joseph J. Kearns c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1942	Trustee	Since August 1994	Senior Adviser, Kearns & Associates LLC (investment consulting); Chairperson of the Audit Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 1994); Director, Rubicorn Investments (since February 2019); formerly, Deputy Chairperson of the Audit Committee (July 2003-September 2006) and Chairperson of the Audit Committee of various Morgan Stanley Funds (since August 1994); CFO of the J. Paul Getty Trust (1982-1999).		87	Prior to August 10, 2016, Director of Electro Rent Corporation (equipment leasing); Prior to December 31, 2013, Director of The Ford Family Foundation.

36

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Address and Birth Year of Independent Trustee	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years and Other Relevant Professional Experience	Number of Funds in Fund Complex Overseen by Independent Trustee**		Other Directorships Held by Independent Trustee***
Michael F. Klein c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1958	Trustee	Since August 2006	Managing Director, Aetos Alternatives Management, LP (since March 2000); Co-President, Aetos Alternatives Management, LP (since January 2004) and Co-Chief Executive Officer of Aetos Alternatives Management, LP (since August 2013); Chairperson of the Fixed Income Sub-Committee of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 2006); formerly, Managing Director, Morgan Stanley & Co. Inc. and Morgan Stanley Dean Witter Investment Management and President, various Morgan Stanley Funds (June 1998-March 2000); Principal, Morgan Stanley & Co. Inc. and Morgan Stanley Dean Witter Investment Management (August 1997-December 1999).		86	Director of certain investment funds managed or sponsored by Aetos Alternatives Management, LP; Director of Sanitized AG and Sanitized Marketing AG (specialty chemicals).
Patricia Maleski c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1960	Trustee	Since January 2017	Managing Director, JPMorgan Asset Management (2004-2016); Oversight and Control Head of Fiduciary and Conflicts of Interest Program (2015-2016); Chief Control Officer-Global Asset Management (2013-2015); President, JPMorgan Funds (2010-2013); Chief Administrative Officer (2004-2013); various other positions including Treasurer and Board Liaison (since 2001).		87	None.
W. Allen Reed c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1947	Chair of the Board and Trustee	Chair of the Boards since August 2020 and Trustee since August 2006	Chair of the Boards of various Morgan Stanley Funds (since August 2020); Chairperson of the Governance Committee; Chairperson of the Equity Sub-Committee of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 2006); formerly, Vice Chair of the Boards of various Morgan Stanley Funds (January 2020-August 2020); President and Chief Executive Officer of General Motors Asset Management; Chairman and Chief Executive Officer of the GM Trust Bank and Corporate Vice President of General Motors Corporation (August 1994-December 2005).		86	Formerly, Director of Legg Mason, Inc. (2006-2019); and Director of the Auburn University Foundation (2010-2015).

*  This is the earliest date the Trustee began serving the Morgan Stanley Funds. Each Trustee serves an indefinite term, until his or her successor is elected.

**  The Fund Complex includes (as of December 31, 2019) all open-end and closed-end funds (including all of their portfolios) advised by Morgan Stanley Investment Management Inc. (the "Adviser") and any funds that have an adviser that is an affiliated person of the Adviser (including, but not limited to, Morgan Stanley AIP GP LP).

***  This includes any directorships at public companies and registered investment companies held by the Trustee at any time during the past five years.

37

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited) (cont'd)

Executive Officers:

Name, Address and Birth Year of Executive Officer	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years
John H. Gernon 522 Fifth Avenue New York, NY 10036 Birth Year 1963	President and Principal Executive Officer	Since September 2013	President and Principal Executive Officer of the Equity and Fixed Income Funds and the Morgan Stanley AIP Funds (since September 2013) and the Liquidity Funds and various money market funds (since May 2014) in the Fund Complex; Managing Director of the Adviser; Head of Public Markets Product Development (since 2006).
Timothy J. Knierim 522 Fifth Avenue New York, NY 10036 Birth Year 1959	Chief Compliance Officer	Since December 2016	Managing Director of the Adviser and various entities affiliated with the Adviser; Chief Compliance Officer of various Morgan Stanley Funds and the Adviser (since December 2016) and Chief Compliance Officer of Morgan Stanley AIP GP LP (since 2014). Formerly, Managing Director and Deputy Chief Compliance Officer of the Adviser (2014-2016); and formerly, Chief Compliance Officer of Prudential Investment Management, Inc. (2007-2014).
Francis J. Smith 522 Fifth Avenue New York, NY 10036 Birth Year 1965	Treasurer and Principal Financial Officer	Treasurer since July 2003 and Principal Financial Officer since September 2002	Managing Director of the Adviser and various entities affiliated with the Adviser; Treasurer (since July 2003) and Principal Financial Officer of various Morgan Stanley Funds (since September 2002).
Mary E. Mullin 522 Fifth Avenue New York, NY 10036 Birth Year 1967	Secretary	Since June 1999	Managing Director of the Adviser; Secretary of various Morgan Stanley Funds (since June 1999).
Michael J. Key 522 Fifth Avenue New York, NY 10036 Birth Year 1979	Vice President	Since June 2017	Vice President of the Equity and Fixed Income Funds, Liquidity Funds, various money market funds and the Morgan Stanley AIP Funds in the Fund Complex (since June 2017); Executive Director of the Adviser; Head of Product Development for Equity and Fixed Income Funds (since August 2013).

*  This is the earliest date the officer began serving the Morgan Stanley Funds. Each officer serves a one-year term, until his or her successor is elected and qualifies.

38

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Adviser and Administrator

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

Distributor

Morgan Stanley Distribution, Inc.
522 Fifth Avenue
New York, New York 10036

Dividend Disbursing and Transfer Agent

DST Asset Manager Solutions, Inc.
2000 Crown Colony Drive
Quincy, Massachusetts 02169

Custodian

State Street Bank and Trust Company
One Lincoln Street
Boston, Massachusetts 02111

Legal Counsel

Dechert LLP
1095 Avenue of the Americas
New York, New York 10036

Counsel to the Independent Trustees

Perkins Coie LLP
1155 Avenue of the Americas,
22nd Floor
New York, New York 10036

Independent Registered Public Accounting Firm

Ernst & Young LLP
200 Clarendon Street
Boston, Massachusetts 02116

Reporting to Shareholders

Each Morgan Stanley fund provides a complete schedule of portfolio holdings in its Semi-Annual and the Annual Reports within 60 days of the end of the fund's second and fourth fiscal quarters. The Semi-Annual and Annual Reports are filed electronically with the Securities and Exchange Commission ("SEC") on Form N-CSRS and Form N-CSR, respectively. Morgan Stanley also delivers the Semi-Annual and Annual Reports to fund shareholders and makes these reports available on its public website, www.morganstanley.com/im/shareholderreports. Each Morgan Stanley non-money market fund also files a complete schedule of portfolio holdings with the SEC for the fund's first and third fiscal quarters as an attachment to Form N-PORT. Morgan Stanley does not deliver the reports for the first and third fiscal quarters to shareholders, nor are the reports posted to the Morgan Stanley public website. However, the holdings for each money market fund are posted to the Morgan Stanley public website. You may obtain the Form N-PORT filings (as well as the Form N-CSR and N-CSRS filings) by accessing the SEC's website, www.sec.gov. You can also request copies of these materials, upon payment of a duplicating fee, by electronic request at the SEC's email address (publicinfo@sec.gov).

Proxy Voting Policies and Procedures and Proxy Voting Record

You may obtain a copy of the Trust's Proxy Voting Policy and Procedures and information regarding how the Trust voted proxies relating to portfolio securities during the most recent twelve-month period ended June 30, without charge, upon request, by calling toll free 1 (800) 548-7786 or by visiting our website at www.morganstanley.com/im/shareholderreports. This information is also available on the SEC's website at www.sec.gov.

This report is authorized for distribution only when preceded or accompanied by a prospectus or summary prospectus of the applicable fund of Morgan Stanley Institutional Fund Trust, which describes in detail the fund's investment policies, risks, fees and expenses. Please read the prospectus carefully before you invest or send money. For additional information, including information regarding the investments comprising the Fund, please visit our website at www.morganstanley.com/im/shareholderreports or call toll free 1 (800) 548-7786.

39

Printed in U.S.A.
This Report has been prepared for shareholders and may be distributed to others only if preceded or accompanied by a current prospectus.

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

© 2020 Morgan Stanley. Morgan Stanley Distribution, Inc.

IFTMCGANN
3298674 EXP 11.30.21

INVESTMENT MANAGEMENT

Morgan Stanley Institutional Fund Trust

Global Strategist Portfolio

Annual Report

September 30, 2020

Beginning on January 1, 2021, as permitted by regulations adopted by the Securities and Exchange Commission ("SEC"), paper copies of the Fund's Annual and Semi-Annual Reports to Shareholders ("Shareholder Reports") will no longer be sent by mail, unless you specifically request paper copies of the Shareholder Reports from the Fund or from your financial intermediary, such as a broker-dealer or a bank. Instead, the Shareholder Reports will be made available on the Fund's website, https://www.morganstanley.com/im/shareholderreports and you will be notified by mail each time a Shareholder Report is posted and provided with a website link to access the Shareholder Report. If you already elected to receive Shareholder Reports electronically, you will not be affected by this change and you need not take any action. You may elect to receive Shareholder Reports and other communications from the Fund electronically anytime by contacting your financial intermediary or, if you are a direct investor, please follow the instructions on the envelope.

Beginning on January 1, 2019, you may elect to receive all future Shareholder Reports in paper free of charge. If you invest through a financial intermediary, you can contact your financial intermediary to request that you continue to receive paper copies of your Shareholder Reports. If you invest directly with the Fund, please follow the instructions on the envelope to let the Fund know you wish to continue receiving paper copies of your Shareholder Reports. Your election to receive Shareholder Reports in paper will apply to all funds held in your account if you invest through your financial intermediary or all funds held with the fund complex if you invest directly with a fund.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Table of Contents

Shareholders' Letter	2
Consolidated Expense Example	3
Investment Overview	4
Consolidated Portfolio of Investments	9
Consolidated Statement of Assets and Liabilities	51
Consolidated Statement of Operations	53
Consolidated Statements of Changes in Net Assets	54
Consolidated Financial Highlights	56
Notes to Consolidated Financial Statements	61
Report of Independent Registered Public Accounting Firm	74
Investment Advisory Agreement Approval	75
Liquidity Risk Management Program	77
Federal Tax Notice	78
Privacy Notice	79
Trustee and Officer Information	81

This report is authorized for distribution only when preceded or accompanied by a prospectus or summary prospectus of the applicable Fund of the Morgan Stanley Institutional Fund Trust. To receive a prospectus and/or statement of additional information ("SAI"), which contains more complete information such as investment objectives, charges, expenses, policies for voting proxies, risk considerations and describes in detail each of the Fund's investment policies to the prospective investor, please call toll free 1 (800) 548-7786. Please read the prospectuses carefully before you invest or send money.

Additionally, you can access information about the Fund, including performance, characteristics and investment team commentary, through Morgan Stanley Investment Management's website: www.morganstanley.com/im/shareholderreports.

Market forecasts provided in this report may not necessarily come to pass. There is no guarantee that any sectors mentioned will continue to perform as discussed herein or that securities in such sectors will be held by the Fund in the future. There is no assurance that a fund will achieve its investment objective. Funds are subject to market risk, which is the possibility that market values of securities owned by the Fund will decline and, therefore, the value of the Fund's shares may be less than what you paid for them. Accordingly, you can lose money investing in this Fund. Please see the prospectus for more complete information on investment risks.

1

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Shareholders' Letter (unaudited)

Dear Shareholders,

We are pleased to provide this Annual Report, in which you will learn how your investment in Global Strategist Portfolio (the "Fund") performed during the latest twelve-month period.

Morgan Stanley Investment Management is a client-centric, investor-led organization. Our global presence, intellectual capital, and breadth of products and services enable us to partner with investors to meet the evolving challenges of today's financial markets. We aim to deliver superior investment service and to empower our clients to make the informed decisions that help them reach their investment goals.

As always, we thank you for selecting Morgan Stanley Investment Management, and look forward to working with you in the months and years ahead.

Sincerely,

John H. Gernon
President and Principal Executive Officer

October 2020

2

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Expense Example (unaudited)

Global Strategist Portfolio

As a shareholder of the Fund, you may incur two types of costs: (1) transactional costs, including sales charge (loads) on purchase payments; and (2) ongoing costs, which may include advisory fees, administration fees, distribution and shareholder services fees; and other Fund expenses. This example is intended to help you understand your ongoing costs (in dollars) of investing in the Fund and to compare these costs with the ongoing costs of investing in other mutual funds.

This example is based on an investment of $1,000 invested at the beginning of the six-month period ended September 30, 2020 and held for the entire six-month period.

Actual Expenses

The table below provides information about actual account values and actual expenses. You may use the information in this table, together with the amount you invested, to estimate the expenses that you paid over the period. Simply divide your account value by $1,000 (for example, an $8,600 account value divided by $1,000 = 8.6), then multiply the result by the number in the table under the heading entitled "Actual Expenses Paid During Period" to estimate the expenses you paid on your account during this period.

Hypothetical Example for Comparison Purposes

The table below provides information about hypothetical account values and hypothetical expenses based on the Fund's actual expense ratio and an assumed rate of return of 5% per year before expenses, which is not the Fund's actual return. The hypothetical account values and expenses may not be used to estimate the actual ending account balance or expenses you paid for the period. You may use this information to compare the ongoing costs of investing in the Fund and other funds. To do so, compare this 5% hypothetical example with the 5% hypothetical examples that appear in the shareholder reports of the other funds.

Please note that the expenses shown in the table are meant to highlight your ongoing costs only and do not reflect any transactional costs, such as sales charges (loads, if applicable). Therefore, the information for each class in the table is useful in comparing ongoing costs only, and will not help you determine the relative total costs of owning different funds. In addition, if these transactional costs were included, your costs would have been higher.

	Beginning Account Value 4/1/20		Actual Ending Account Value 9/30/20		Hypothetical Ending Account Value		Actual Expenses Paid During Period*		Hypothetical Expenses Paid During Period*		Net Expense Ratio During Period**
Global Strategist Portfolio Class I	$	1,000.00	$	1,209.90	$	1,021.45	$	3.92	$	3.59		0.71	%
Global Strategist Portfolio Class A		1,000.00		1,208.00		1,019.95		5.58		5.10		1.01
Global Strategist Portfolio Class L		1,000.00		1,204.50		1,017.30		8.49		7.77		1.54
Global Strategist Portfolio Class C		1,000.00		1,202.60		1,015.95		9.97		9.12		1.81
Global Strategist Portfolio Class IS		1,000.00		1,209.60		1,021.55		3.81		3.49		0.69

*  Expenses are calculated using each Fund Class' annualized net expense ratio (as disclosed), multiplied by the average account value over the period and multiplied by 183/366 (to reflect the most recent one-half year period).

**  Annualized.

3

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Overview (unaudited)

Global Strategist Portfolio

The Fund seeks above-average total return over a market cycle of three to five years.

Performance

For the fiscal year ended September 30, 2020, the Fund's Class I shares had a total return based on net asset value and reinvestment of distributions per share of 5.93%, net of fees. The Fund's Class I shares underperformed against the Fund's primary benchmark, the MSCI All Country World Index, which returned 10.44%, and underperformed the Customized MSIM Global Allocation Index (the "Customized Index"), which returned 9.26%.

Factors Affecting Performance¹

•  In the 12 months ended September 30, 2020, equities outperformed bonds and commodities, with the MSCI All Country World Index (ACWI) up +10.4%, the J.P. Morgan Global Government Bond Index up +6.7%, and the S&P GSCI Index, a broad index of commodity prices, down –27.8%.² (Except where noted, equity market returns are represented by the MSCI regional or country index and are calculated in U.S. dollars [USD].)

•  Global markets ended 2019 on a strong risk-on note, propelled by stabilizing economic data, subdued inflation, news of a U.S.-China phase one trade deal, and 75 basis points of Federal Reserve (Fed) easing. Then the COVID-19 pandemic began spreading, causing major economies around the world to grind to a near-halt and global markets to sell off, prompting policy makers to come out forcefully with fiscal and monetary support in the spring and summer of 2020. Policy support, coupled with gradual economic reopening, eventually led to improving growth and sharply rebounding markets for the remainder of the fiscal year ending in September 2020.

•  Global equities rose +10.4% for the fiscal year overall, but experienced substantial volatility on the way (MSCI ACWI in USD). After rising by

+11.9% from September 30, 2019, to February 19, 2020, global equity prices fell by over one third in the next 33 days, before rebounding by +48% from March 23 to September 30, 2020 (MSCI ACWI in USD). The VIX Index climbed above 80 in early March 2020, a level it has not reached since 2008, with the S&P 500 Index subsequently experiencing its best two-quarter performance since 2009. U.S. equities led other regions (S&P 500 Index +15.1% in the fiscal year period), supported by bold government stimulus and positive economic surprises. Positive performance was driven in particular by U.S. mega-cap and growth stocks that have dominated for much of the last market cycle. The S&P 500 tech and consumer discretionary sectors were up +48.6% and 40.0%, respectively, while the energy and financials sectors were down –45.3% and –12.5%. Eurozone equities were the weakest regionally (Eurostoxx 50 Index –8.6% in euro terms). While data there was surprising positively in the fourth quarter of 2019, the region was hit relatively early by the COVID-19 virus. The region managed to contain the virus quickly with aggressive lockdowns and many individual countries announced fiscal stimulus plans, but coordinated policy support proved to be more difficult to achieve, and the region began to experience a second wave by early fall 2020, prompting fears of renewed shutdowns. Emerging markets rose in line with the global index (MSCI Emerging Markets Index in USD +10.5%), despite difficulty containing the virus, aided in part by a weaker U.S. dollar and overall risk-on sentiment.

•  Prices on relatively safe government bonds rose +6.7%, with gains primarily coming at the height of COVID-19 fears in the first quarter of 2020 (J.P. Morgan Global Government Bond Index). Even as economic data improved, U.S. sovereign bond yields did not rise with equity prices in the second and third quarters of 2020, reflecting lingering investor caution as COVID-19 cases remained

¹  Certain of the Fund's investment themes may, in whole or part, be implemented through the use of derivatives, including the purchase and sale of futures, options, swaps, structured investments (including commodity-linked notes) and other related instruments and techniques. The Fund may also invest in foreign currency forward exchange contracts, which are also derivatives, in connection with its investments in foreign securities. The Fund may use derivative instruments for a variety of purposes, including hedging, risk management, portfolio management or to earn income. As a result, the use of derivatives had a material effect on the Fund's performance during the period.

²  Data sources used in preparation of this commentary include FactSet and Bloomberg LP. data as of September 30, 2020.

4

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Overview (unaudited) (cont'd)

Global Strategist Portfolio

elevated globally. The yield curve steepened: the U.S. 10-year Treasury yield fell –98 basis points to 0.68% while the 2-year fell –127 basis points to 0.13%. Riskier spreads followed a similar pattern to equities, widening sharply in the first quarter of 2020 then rebounding with overall sentiment in the second and third quarters. U.S. high yield bonds suffered a major sell-off before the U.S. announced a comprehensive economic support package that included support for high yield markets. Spreads shot upward from about 375 basis points in September 2019 to 1100 basis points on March 23, 2020, before settling back down to 517 basis points by the end of the fiscal year (Bloomberg Barclays U.S. Corporate High Yield Index), ending September 2020 about 140 basis points wider than their pre-COVID levels. Emerging market hard currency bond spreads nearly roundtripped during the year: rising from 338 to 662 basis points on March 23, 2020, then falling back down to end the fiscal year just below 400 basis points (J.P. Morgan Emerging Markets Bond Index Global).

•  Commodity prices overall collapsed –27.8% (S&P GSCI Index), driven by oil prices. Brent oil prices fell from $60 per barrel to just over $21 per barrel, as the OPEC+ alliance (between the Organization of Petroleum Exporting Countries and key oil-producing non-OPEC members) broke down and Saudi Arabia increased production amid a collapse in global demand. Prices reached their lowest point when concerns about oversupply and storage limitations caused WTI oil futures for May delivery to fall to –$37.63 per barrel before rebounding. Oil prices managed to rebound by over 90% (entirely in the second quarter of 2020), ending the fiscal year just above $40 per barrel. Gold has been among the best performing assets during the fiscal year, given its role as a relatively safe asset, and rose +28.1%.

•  The U.S. dollar weakened by –5.5%, despite a temporary spike amid funding concerns in late March 2020. From the March peak, the U.S. dollar has now fallen by –8.9%, given stabilizing global economic data and aggressive U.S. fiscal and monetary activism. Relatively safe reserve currencies were the largest gainers versus the U.S. dollar, with the Swiss franc up +8.4% and the euro up +7.5%. The renminbi began appreciating in June 2020, and rose +5.3% versus the U.S. dollar for the fiscal year,

as China's ability to contain the virus and its post-COVID economic rebound both beat expectations and its macro policy remained supportive. However, emerging market currencies overall depreciated during the fiscal year (J.P. Morgan Emerging Market Currency Index –10%). The weakest were the Turkish lira, which fell –27%; the Brazilian real, which was down –26%; and the Argentine peso, which fell –25%.

•  Regarding the Fund's overall performance relative to the Customized Index, the Fund's asset allocation mix of an average overweight in equities, an underweight in fixed income and an overweight in cash had a negative impact on performance.

•  Active positions within equities contributed negatively to performance. Detractors included positions in our Value Recovery theme, such as overweight value stocks vs. anti-value, low-volatility and momentum stocks in the U.S. and Europe. In addition, an overweight position in Japanese real estate relative to Japanese equities and an overweight position in European domestic stocks relative to U.S. equities also detracted from performance. However, these losses were partially offset by gains from an overweight position in U.S. homebuilders and housing stocks relative to U.S. equities, an overweight position in U.S. equity volatility (beta hedged), and an underweight position in Australian banks relative to developed market equities and banks.

•  Active positions within fixed income contributed positively to performance. Contributors during the period included an overweight position in U.S. 10-year inflation breakeven rates and an overweight position in Greek 10-year bonds versus French, Italian and Spanish 10-year bonds. Detractors during the period included an underweight position in U.S. 30-year Treasuries and an overweight position in Mexican 10-year bonds relative to U.S. 10-year Treasuries.

•  Active positions within commodities had a positive impact on performance, as overweight positions in gold and oil contributed to performance.

•  Active currency positions (implemented via currency forwards and futures) negatively impacted performance. Overweight positions in the Mexican

5

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Overview (unaudited) (cont'd)

Global Strategist Portfolio

peso and in the British pound, both relative to the U.S. dollar, and in the Brazilian real relative to emerging market currencies detracted from performance. These losses were partially offset by gains from our overweight positions in defensive currencies (Swiss franc, euro, British pound and Japanese yen) and in the Chinese renminbi, both relative to the U.S. dollar, and in the Argentine peso relative to emerging market currencies.

Management Strategies

•  We expect continued steady improvement in economic activity, as the impact of the virus subsides and as economic stimulus remains strong. In spite of the near-term risks of rolling second waves and some renewed lockdowns, between now and mid-2021 we expect a gradual return to some semblance of normalcy. We enter the fourth quarter of 2020 with a modest tactical overweight to global equities. We think bonds are at risk in a recovery, and express this view via a curve steepener position. We have re-established a significant overweight in value stocks vs. low volatility and anti-value stocks in the U.S., and remain overweight underpriced recovery plays, such as U.S. housing stocks, global industrials and auto manufacturers, as well as developed market hotel stocks. We are also underweight certain COVID "winners" and U.S. initial public offering stocks. Key risks to our views are mostly to the downside, and include the increasing likelihood of a second wave and the lack of a vaccine by early 2021. Other downside risks that we are watching include a fiscal cliff, a Democratic sweep, and worsening U.S.-China relations. Upside risks are greater fiscal activism and/or a weaker U.S. dollar.

•  We are neutral duration, but hold a curve steepener position. As economies reopen and fiscal stimulus increases, we believe a curve steepener is likely to benefit from a growth and inflation recovery. Positive carry makes a long-end curve steepener more attractive relative to an outright underweight position in Treasuries. We believe recessionary fundamentals are more than fully priced in government bonds, and going forward we expect the U.S. 10-year Treasury yield to rise modestly from 0.77% to 1.1% by the second half of 2020. We believe U.S. growth will come in at –2.4% in 2020 and +6.7% in 2021 (versus consensus

expectations of –4.0% in 2020 and +3.7% in 2021). In addition, we believe inflation will rebound modestly faster than consensus forecasts in a period of extreme monetary policy accommodation, with core personal consumption expenditures coming in at 1.8% in 12 months versus consensus expectation of 1.6% by third quarter 2021. Elsewhere in fixed income, we are overweight U.S. TIPS (Treasury inflation-protected securities) vs. Treasuries. Rates markets are pricing in approximately 1.5% U.S. core inflation over the next 10 years. As economic activity rebounds, we expect resilient aggregate demand, given massive fiscal and monetary stimulus, to be met with shrunken supply as the labor market recovers more gradually. Deficit spending will necessitate some form of financial repression, with higher inflation likely being a major part of this.

•  We are modestly overweight U.S. equities. While valuations in absolute terms are very high at 21.9x forward price-to-earnings for U.S. equities, U.S. stocks are still somewhat cheap relative to bonds (equity risk premium 4.58%), and we expect the equity risk premium could overshoot in a recovery, compressing beyond normalized levels of around 4.2%, closer to 3.5%, as the equity risk premium tends to overshoot during recoveries. Fundamentals are supportive: a strong earnings per share (EPS) rebound is currently underway, and should continue with reopenings and an eventual normalization. While U.S. EPS is likely to be down by –21% for the year, we expect that full year 2021 EPS will grow by +25% year-over-year, in line with consensus expectations.

•  We are overweight value stocks vs. low volatility and anti-value stocks in the U.S., where value is still near the cheapest it has ever been, and positioning is extreme. For example, U.S. value stocks are –39% cheap to their long-term median relative valuation to anti-value, compared with 40% in March 2000. The expected bottoming in economic activity should benefit value stocks relative to anti-value and low volatility stocks.

•  We believe the U.S. dollar is in the early stages of a multi-year bear market. While better growth in the U.S., coupled with global economic uncertainty, have buoyed the U.S. dollar's role as a relative safe-haven asset and caused it to appreciate versus other

6

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Overview (unaudited) (cont'd)

Global Strategist Portfolio

reserve currencies, the U.S. dollar remains expensive, and is facing headwinds in the medium term. We expect the dollar to depreciate approximately 10% over the next 12 to 18 months.

•  We are overweight commodities, via gold and oil. We believe that the medium-term outlook for gold continues to be favorable as the fiscal response to the COVID-19 outbreak has been to flood the economy with money, while the Fed has promised to keep interest rates at zero for a prolonged period, even after inflation has risen. Historically, money printing and negative real interest rates have been extremely favorable for gold on a forward-looking basis, and we expect the same to hold true going forward. Our end-2021 forecast is for gold above $2,100 per ounce. We expect oil prices will increase to $60 per barrel by mid-2021 from around $40 today, as demand recovers and oil inventories fall back to pre-COVID-19 levels. Nearer-term risks to the downside include moderating demand in the event of slowing global mobility, and the possibility that OPEC+ reverses current production cuts early next year.

*  Minimum Investment

In accordance with SEC regulations, the Fund's performance shown assumes that all recurring fees (including management fees) were deducted and all dividends and distributions were reinvested. The performance of Class A, Class L, Class C and Class IS shares will vary from the performance of Class I shares based upon their different inception dates and will be negatively impacted by additional fees assessed to those classes (where applicable).

7

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Overview (unaudited) (cont'd)

Global Strategist Portfolio

Performance Compared to the MSCI All Country World Index⁽¹⁾, the Customized MSIM Global Allocation Index⁽²⁾ and the Lipper Flexible Portfolio Funds Index⁽³⁾

	Period Ended September 30, 2020 Total Returns(4)
				Average Annual
	One Year			Five Years			Ten Years			Since Inception(10)
Fund — Class I Shares w/o sales charges(5)		5.93	%		6.76	%		6.80	%		7.07	%
Fund — Class A Shares w/o sales charges(6)		5.65			6.42			6.48			6.04
Fund — Class A Shares with maximum 5.25% sales charges(6)		0.09			5.29			5.91			5.80
Fund — Class L Shares w/o sales charges(7)		5.10			5.89			—			5.12
Fund — Class C Shares w/o sales charges(8)		4.81			5.57			—			3.08
Fund — Class C Shares with maximum 1.00% deferred sales charges(8)		3.81			5.57			—			3.08
Fund — Class IS Shares w/o sales charges(9)		6.02			6.81			—			4.56
MSCI All Country World Index		10.44			10.30			8.55			7.67
Customized MSIM Global Allocation Index		9.26			7.77			5.91			—
Lipper Flexible Portfolio Funds Index		11.52			8.56			7.56			6.93

Performance data quoted represents past performance, which is no guarantee of future results, and current performance may be lower or higher than the figures shown. Performance assumes that all dividends and distributions, if any, were reinvested. For the most recent month-end performance figures, please visit www.morganstanley.com/im/shareholderreports. Investment returns and principal value will fluctuate so that Fund shares, when redeemed, may be worth more or less than their original cost. Total returns do not reflect the deduction of taxes that a shareholder would pay on Fund distributions or the redemption of Fund shares. Performance of share classes will vary due to differences in sales charges and expenses.

⁽¹⁾  The MSCI All Country World Index (ACWI) is a free float-adjusted market capitalization weighted index designed to measure the equity market performance of developed and emerging markets. The term "free float" represents the portion of shares outstanding that are deemed to be available for purchase in the public equity markets by investors. The performance of the Index is listed in U.S. dollars and assumes reinvestment of net dividends. Net total return indices reinvest dividends after the deduction of withholding taxes, using (for international indices) a tax rate applicable to non-resident institutional investors who do not benefit from double taxation treaties. Returns, including periods prior to January 1, 2001, are calculated using the return data of the MSCI All Country World Index (gross dividends) through December 31, 2000 and the return data of the MSCI All Country World Index (net dividends) after December 31, 2000. The Index is unmanaged and its returns do not include any sales charges or fees. Such costs would lower performance. It is not possible to invest directly in an index.

⁽²⁾  The Customized MSIM Global Allocation Index is a performance linked benchmark comprised of 60% MSCI All Country World Index and 40% Bloomberg Barclays Global Aggregate Index for periods after May 31, 2017. Prior to May 31, 2017, the Customized MSIM Global Allocation Index consisted of 60% MSCI All Country World Index (benchmark that measures the equity market performance of developed and emerging markets), 30% Bloomberg Barclays Global Aggregate Index (benchmark that provides a broadbased measure of the global investment grade fixed-rate debt markets), 5% S&P GSCI Light Energy Index (benchmark for investment performance in the energy commodity market) and 5% ICE BofA U.S. Dollar 1-Month LIBID Average Index (benchmark that tracks the performance of a basket of synthetic assets paying LIBID to a stated maturity). The Customized MSIM Global Allocation Index was added as the Fund benchmark on October 2, 2013 and is provided for comparative purposes only. The Index is unmanaged and its returns do not include any sales charges or fees. Such costs would lower performance. It is not possible to invest directly in an index.

⁽³⁾  The Lipper Flexible Portfolio Funds Index is an equally weighted performance index of the largest qualifying funds (based on net assets) in the Lipper Flexible Portfolio Funds classification. The Index, which is adjusted for capital gains distributions and income dividends, is unmanaged and should not be considered an investment. There are currently 30 funds represented in this Index. As of the date of this report, the Fund was in the Lipper Flexible Portfolio Funds classification.

⁽⁴⁾  Total returns for the Fund reflect expenses waived and/or reimbursed, if applicable, by the Adviser. Without such waivers and/or reimbursements, total returns would have been lower.

⁽⁵⁾  Commenced operations on December 31, 1992.

⁽⁶⁾  Commenced offering on November 1, 1996.

⁽⁷⁾  Commenced offering on April 27, 2012.

⁽⁸⁾  Commenced offering on April 30, 2015.

⁽⁹⁾  Commenced offering on May 29, 2015.

⁽¹⁰⁾  For comparative purposes, average annual since inception returns listed for the Indexes refer to the inception date of Class I of the Fund, not the inception of the Indexes.

8

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments

Global Strategist Portfolio

	Face Amount (000)		Value (000)
Fixed Income Securities (40.2%)
Agency Adjustable Rate Mortgage (0.0%)
United States (0.0%)
Federal Home Loan Mortgage Corporation,
Conventional Pool:,
12 Month USD LIBOR + 1.62%, 3.00%, 7/1/45	$	67	$	69
Agency Fixed Rate Mortgages (3.6%)
United States (3.6%)
Federal Home Loan Mortgage Corporation,
Conventional Pool:
4.50%, 1/1/49		305		331
Gold Pools:
3.50%, 1/1/44 - 6/1/45		906		991
4.50%, 1/1/49		70		74
6.50%, 5/1/32 - 7/1/32		28		30
7.50%, 5/1/35		3		4
Federal National Mortgage Association,
Conventional Pools:
3.00%, 7/1/49		654		680
3.50%, 3/1/47		118		127
4.00%, 4/1/45 - 9/1/45		862		948
4.50%, 3/1/41 - 11/1/44		186		207
5.00%, 1/1/41 - 3/1/41		447		514
6.00%, 1/1/38		3		4
6.50%, 12/1/29		9		10
7.00%, 2/1/31		54		56
7.50%, 8/1/37		6		7
October TBA:
2.00%, 10/1/50 (a)		1,000		1,034
3.00%, 10/1/35 - 10/1/50 (a)		5,400		5,657
3.50%, 10/1/50 (a)		2,000		2,109
Government National Mortgage Association,
Various Pools:
4.00%, 8/20/41 - 11/20/42		251		276
4.50%, 6/20/49		121		127
5.00%, 2/20/49 - 6/20/49		366		392
5.50%, 8/15/39		16		18
				13,596
Asset-Backed Securities (0.5%)
United States (0.5%)
Freed ABS Trust,
3.06%, 3/18/27 (b)		300		300
New Century Home Equity Loan Trust,
1 Month USD LIBOR + 1.35%, 1.50%, 3/25/33 (c)		205		203
NovaStar Mortgage Funding Trust,
1 Month USD LIBOR + 1.58%, 1.72%, 12/25/34 (c)		200		197
Renaissance Home Equity Loan Trust,
1 Month USD LIBOR + 0.76%, 0.91%, 12/25/32 (c)		227		219

	Face Amount (000)		Value (000)
SASCO Mortgage Loan Trust,
1 Month USD LIBOR + 2.18%, 2.32%, 5/25/34 (c)	$	360	$	360
SLM Student Loan Trust,
3 Month EURIBOR + 0.55%, 0.10%, 7/25/39 (c)	EUR	450		501
				1,780
Collateralized Mortgage Obligations — Agency Collateral Series (0.0%)
United States (0.0%)
Federal Home Loan Mortgage Corporation
IO REMIC,
6.05% - 1 Month USD LIBOR, 5.90%, 4/15/39 (d)	$	15		—	@
Commercial Mortgage-Backed Securities (0.5%)
United Kingdom (0.1%)
Taurus 2018-2 UK DAC,
3 Month GBP LIBOR + 1.10%, 1.17%, 5/22/28 (c)	GBP	231		291
United States (0.4%)
Ashford Hospitality Trust,
1 Month USD LIBOR + 1.85%, 2.00%, 6/15/35 (b)(c)	$	250		227
COMM Mortgage Trust,
3.28%, 1/10/46		305		318
4.88%, 7/15/47 (b)(c)		152		121
Federal Home Loan Mortgage Corporation,
2.79%, 1/25/22		69		71
2.97%, 10/25/21		82		84
JP Morgan Chase Commercial Mortgage Securities Trust,
4.39%, 7/15/46 (b)		29		29
UBS-Barclays Commercial Mortgage Trust,
3.53%, 5/10/63		255		263
WFRBS Commercial Mortgage Trust,
4.14%, 10/15/57 (b)(c)		362		317
5.19%, 9/15/46 (b)(c)		375		225
				1,655
				1,946
Corporate Bonds (10.9%)
Australia (0.2%)
Macquarie Bank Ltd.,
6.63%, 4/7/21 (b)		270		278
Macquarie Group Ltd.,
4.15%, 3/27/24 (b)		125		134
Transurban Finance Co. Pty Ltd.,
2.00%, 8/28/25		350		433
				845
Belgium (0.1%)
Anheuser-Busch InBev SA,
2.75%, 3/17/36	EUR	350		481
Canada (0.6%)
Enbridge, Inc.,
2.50%, 1/15/25	$	200		210
Province of British Columbia Canada,
2.00%, 10/23/22		780		808

The accompanying notes are an integral part of the consolidated financial statements.
9

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

	Face Amount (000)		Value (000)
Canada (cont'd)
Province of Ontario Canada,
2.30%, 6/15/26	$	780	$	852
Royal Bank of Canada,
2.75%, 2/1/22		350		362
				2,232
Chile (0.1%)
Banco del Estado de Chile,
2.67%, 1/8/21 (b)		300		302
China (0.1%)
Baidu, Inc.,
2.88%, 7/6/22		200		206
Colombia (0.2%)
Ecopetrol SA,
5.88%, 9/18/23		710		782
Denmark (0.1%)
Danske Bank A/S,
5.00%, 1/12/23 (b)		200		210
France (0.7%)
Banque Federative du Credit Mutuel SA,
0.75%, 7/17/25	EUR	400		486
BNP Paribas SA,
1.13%, 6/11/26		485		591
BPCE SA,
5.15%, 7/21/24 (b)	$	725		813
Orange SA,
5.00%, 10/1/26 (e)	EUR	250		347
TOTAL SA,
2.71%, 12/29/49 (e)		100		121
3.88%, 12/29/49 (e)		250		307
				2,665
Germany (0.8%)
Bayer US Finance II LLC,
3.88%, 12/15/23 (b)	$	675		738
Daimler Finance North America LLC,
2.70%, 6/14/24 (b)		325		344
Deutsche Telekom International Finance BV,
3.60%, 1/19/27 (b)		625		701
Kreditanstalt fuer Wiederaufbau,
1.13%, 9/15/32	EUR	640		870
Muenchener Rueckversicherungs- Gesellschaft AG in Muenchen,
6.00%, 5/26/41		400		486
				3,139
Hong Kong (0.1%)
CK Hutchison International 16 Ltd.,
1.88%, 10/3/21 (b)	$	200		202
India (0.2%)
ONGC Videsh Vankorneft Pte Ltd.,
3.75%, 7/27/26		820		856

	Face Amount (000)		Value (000)
Ireland (0.1%)
Avolon Holdings Funding Ltd.,
2.88%, 2/15/25 (b)	$	250	$	230
Israel (0.0%)
Teva Pharmaceutical Finance Netherlands III BV,
2.20%, 7/21/21		82		81
Korea, Republic of (0.3%)
Korea Electric Power Corp.,
2.50%, 6/24/24 (b)		610		646
Korea Hydro & Nuclear Power Co., Ltd.,
3.75%, 7/25/23 (b)		510		553
				1,199
Netherlands (0.3%)
ASR Nederland N.V.,
5.00%, 9/30/24 (e)	EUR	425		554
Cooperatieve Rabobank UA,
3.95%, 11/9/22	$	250		266
Series G 3.75%, 11/9/20	EUR	300		353
				1,173
Saudi Arabia (0.1%)
Saudi Arabian Oil Co.,
3.50%, 4/16/29	$	490		540
Spain (0.4%)
Banco Santander SA,
3.13%, 1/19/27	EUR	400		521
5.18%, 11/19/25	$	600		680
CaixaBank SA,
0.75%, 4/18/23	EUR	400		477
				1,678
Switzerland (0.3%)
Syngenta Finance N.V.,
4.44%, 4/24/23 (b)	$	200		212
UBS Group Funding Switzerland AG,
3.49%, 5/23/23 (b)		900		939
				1,151
United Arab Emirates (0.1%)
ADCB Finance Cayman Ltd.,
4.00%, 3/29/23 (b)		200		213
United Kingdom (1.0%)
BAT Capital Corp.,
3.56%, 8/15/27		525		568
BP Capital Markets PLC,
2.50%, 11/6/22		275		286
HSBC Holdings PLC,
2.63%, 11/7/25		525		547
4.25%, 3/14/24		400		429
Lloyds Banking Group PLC,
2.44%, 2/5/26		350		363
Nationwide Building Society,
3.77%, 3/8/24 (b)		300		319
4.36%, 8/1/24 (b)		200		217

The accompanying notes are an integral part of the consolidated financial statements.
10

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

	Face Amount (000)		Value (000)
United Kingdom (cont'd)
NGG Finance PLC,
5.63%, 6/18/73	GBP	200	$	292
Royal Bank of Scotland Group PLC,
3.88%, 9/12/23	$	750		805
				3,826
United States (5.1%)
AbbVie, Inc.,
3.20%, 11/21/29 (b)		300		332
Air Lease Corp.,
2.30%, 2/1/25		300		295
Amazon.com, Inc.,
4.25%, 8/22/57		175		240
American International Group, Inc.,
4.88%, 6/1/22		400		429
American Tower Corp.,
2.40%, 3/15/25		200		212
AT&T, Inc.,
1.80%, 9/5/26	EUR	400		505
Bank of America Corp.MTN,
4.00%, 1/22/25	$	825		920
Boeing Co. (The),
5.15%, 5/1/30		525		592
Burlington Northern Santa Fe LLC,
4.55%, 9/1/44		195		255
Campbell Soup Co.,
2.38%, 4/24/30		200		208
Capital One Financial Corp.,
3.30%, 10/30/24		325		353
Charter Communications Operating LLC/ Charter Communications Operating Capital,
5.75%, 4/1/48		175		219
Chubb INA Holdings, Inc.,
0.88%, 6/15/27	EUR	400		482
Cigna Corp.,
2.40%, 3/15/30	$	75		78
3.88%, 10/15/47		200		223
Citigroup, Inc.,
2.57%, 6/3/31		50		52
2.67%, 1/29/31		156		165
2.98%, 11/5/30		94		102
5.50%, 9/13/25		425		504
Comcast Corp.,
1.95%, 1/15/31		400		412
3.40%, 4/1/30		125		145
Crown Castle International Corp.,
3.30%, 7/1/30		125		137
CVS Health Corp.,
3.75%, 4/1/30		50		57
4.10%, 3/25/25		73		83
Deere & Co.,
3.10%, 4/15/30		100		114

	Face Amount (000)		Value (000)
Diamondback Energy, Inc.,
2.88%, 12/1/24	$	425	$	431
Emerson Electric Co.,
1.25%, 10/15/25	EUR	450		560
Energy Transfer Operating LP,
2.90%, 5/15/25	$	600		604
Enterprise Products Operating LLC,
3.95%, 1/31/60		100		99
Ford Motor Credit Co. LLC,
3.09%, 1/9/23		300		295
Fox Corp.,
4.71%, 1/25/29		175		210
GE Capital International Funding Co. Unlimited Co.,
4.42%, 11/15/35		250		264
Georgia-Pacific LLC,
2.30%, 4/30/30 (b)		325		346
Goldman Sachs Group, Inc. (The),
2.88%, 10/31/22		350		358
HCA, Inc.,
5.50%, 6/15/47		100		124
HSBC USA, Inc.,
3.50%, 6/23/24		100		108
JPMorgan Chase & Co.,
3.70%, 5/6/30		200		230
Las Vegas Sands Corp.,
3.20%, 8/8/24		75		76
3.50%, 8/18/26		125		127
Level 3 Financing, Inc.,
3.40%, 3/1/27 (b)		425		459
McDonald's Corp.MTN,
3.38%, 5/26/25		275		306
Metropolitan Life Global Funding I,
2.95%, 4/9/30 (b)		425		478
Newmont Corp.,
3.70%, 3/15/23		26		27
NextEra Energy Capital Holdings, Inc.,
2.25%, 6/1/30		325		337
2.75%, 5/1/25		450		487
NIKE, Inc.,
2.85%, 3/27/30		275		309
NiSource, Inc.,
3.60%, 5/1/30		175		200
NVIDIA Corp.,
2.85%, 4/1/30		275		310
Occidental Petroleum Corp.,
3.20%, 8/15/26		40		32
5.55%, 3/15/26		350		318
Oracle Corp.,
2.95%, 4/1/30		350		392
3.40%, 7/8/24		175		192
Pacific Gas and Electric Co.,
2.50%, 2/1/31		300		286

The accompanying notes are an integral part of the consolidated financial statements.
11

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

	Face Amount (000)		Value (000)
United States (cont'd)
PepsiCo, Inc.,
2.63%, 4/28/26	EUR	400	$	538
Prologis Euro Finance LLC,
1.88%, 1/5/29		300		392
Synchrony Bank,
3.00%, 6/15/22	$	875		903
Target Corp.,
2.65%, 9/15/30		125		140
TJX Cos., Inc. (The),
3.88%, 4/15/30		350		416
Union Pacific Corp.,
3.95%, 9/10/28		190		225
Verizon Communications, Inc.,
4.67%, 3/15/55	EUR	196		273
Walt Disney Co. (The),
2.65%, 1/13/31	$	350		379
Wells Fargo & Co.,
2.57%, 2/11/31		350		368
2.88%, 10/30/30		175		188
5.01%, 4/4/51		300		413
				19,314
				41,325
Mortgages — Other (0.6%)
Netherlands (0.1%)
E-MAC NL 2006-II BV,
3 Month EURIBOR + 0.13%, 0.77%, 1/25/39 (c)	EUR	242		262
United Kingdom (0.1%)
Great Hall Mortgages No 1 PLC,
3 Month EURIBOR + 0.25% 0.00%, 6/18/38 (c)	EUR	200		220
United States (0.4%)
Banc of America Alternative Loan Trust,
5.86%, 10/25/36	$	27		12
6.00%, 4/25/36		1		1
ChaseFlex Trust,
6.00%, 2/25/37		23		15
Federal Home Loan Mortgage Corporation,
3.00%, 9/25/45 - 5/25/47		810		829
3.50%, 5/25/45 - 7/25/46		313		322
4.00%, 5/25/45		32		33
GSR Mortgage Loan Trust,
5.75%, 1/25/37		11		10
Lehman Mortgage Trust,
6.50%, 9/25/37		19		10
Seasoned Credit Risk Transfer Trust,
3.00%, 7/25/58 - 10/25/58		385		422
4.00%, 10/25/58		46		51
				1,705
				2,187

	Face Amount (000)		Value (000)
Sovereign (22.1%)
Australia (1.1%)
Australia Government Bond,
0.25%, 11/21/25	AUD	2,480	$	1,767
2.50%, 5/21/30		1,790		1,487
2.75%, 11/21/29		830		699
3.00%, 3/21/47		340		315
				4,268
Austria (0.1%)
Republic of Austria Government Bond,
0.00%, 2/20/30 (b)	EUR	260		315
2.10%, 12/31/99 (b)		60		150
				465
Belgium (0.4%)
Kingdom of Belgium Government Bond,
0.90%, 6/22/29 (b)		120		157
1.70%, 6/22/50 (b)		350		561
1.90%, 6/22/38 (b)		550		849
				1,567
Canada (1.4%)
Canadian Government Bond,
2.25%, 6/1/29	CAD	4,970		4,289
Province of Quebec Canada,
1.35%, 5/28/30	$	860		884
				5,173
Chile (0.1%)
Chile Government International Bond,
3.50%, 1/25/50		320		366
China (1.3%)
China Development Bank,
3.07%, 3/10/30	CNY	4,900		682
China Government Bond,
3.13%, 11/21/29		20,150		2,945
3.86%, 7/22/49		6,000		883
Sinopec Group Overseas Development 2013 Ltd.,
2.63%, 10/17/20	EUR	300		352
				4,862
Denmark (0.1%)
Denmark Government Bond,
0.50%, 11/15/27	DKK	2,190		370
Finland (0.1%)
Finland Government Bond,
1.13%, 4/15/34 (b)	EUR	270		374
France (1.0%)
French Republic Government Bond OAT,
0.00%, 11/25/29		2,220		2,680
2.00%, 5/25/48 (b)		680		1,147
				3,827

The accompanying notes are an integral part of the consolidated financial statements.
12

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

	Face Amount (000)		Value (000)
Germany (1.0%)
Bundesrepublik Deutschland Bundesanleihe,
0.25%, 2/15/29	$	1,580	$	1,990
4.25%, 7/4/39		210		464
State of North Rhine-Westphalia Germany,
1.65%, 2/22/38		940		1,406
				3,860
Greece (2.6%)
Hellenic Republic Government Bond,
3.75%, 1/30/28		6,812		9,676
Hong Kong (0.1%)
Hong Kong Government International Bond,
2.50%, 5/28/24 (b)	$	250		264
Hungary (0.0%)
Hungary Government Bond,
3.00%, 8/21/30	HUF	17,000		59
Indonesia (0.3%)
Indonesia Government International Bond,
1.75%, 4/24/25	EUR	440		533
Indonesia Treasury Bond,
6.13%, 5/15/28	IDR	2,681,000		174
8.25%, 5/15/29		1,320,000		97
8.38%, 3/15/34		3,345,000		242
				1,046
Italy (1.1%)
Italy Buoni Poliennali Del Tesoro,
1.40%, 5/26/25 (b)	EUR	199		244
1.75%, 7/1/24		1,875		2,336
1.80%, 3/1/41 (b)		260		320
2.45%, 9/1/50 (b)		910		1,241
				4,141
Japan (4.0%)
Japan Government Ten Year Bond,
0.10%, 6/20/26 - 6/20/29	JPY	650,000		6,237
Japan Government Thirty Year Bond,
0.30%, 6/20/46		214,000		1,924
0.40%, 9/20/49		108,000		975
1.70%, 6/20/33		267,000		3,024
2.00%, 9/20/40		253,000		3,132
				15,292
Korea, Republic of (0.2%)
Export-Import Bank of Korea,
2.38%, 6/25/24	$	510		540
Korea International Bond,
2.00%, 6/19/24		350		367
				907
Malaysia (0.4%)
Malaysia Government Bond,
3.96%, 9/15/25	MYR	2,600		675
Petronas Capital Ltd.,
3.50%, 3/18/25 (b)	$	675		743
				1,418

	Face Amount (000)		Value (000)
Mexico (2.5%)
Mexican Bonos,
7.50%, 6/3/27	MXN	12,000	$	604
Series M 7.75%, 5/29/31		5,000		255
8.50%, 5/31/29		156,000		8,349
Mexico Government International Bond,
4.50%, 4/22/29	$	330		371
Petroleos Mexicanos,
6.95%, 1/28/60 (b)		95		73
				9,652
Netherlands (0.4%)
Nederlandse Waterschapsbank,
1.00%, 5/28/30 (b)		376		378
Netherlands Government Bond,
0.00%, 7/15/30 (b)		700		854
2.75%, 1/15/47 (b)		70		144
				1,376
New Zealand (0.3%)
New Zealand Government Bond,
2.75%, 4/15/37	NZD	1,360		1,155
3.00%, 4/20/29		130		105
				1,260
Nigeria (0.1%)
Africa Finance Corp.,
4.38%, 4/17/26 (b)	$	200		216
Norway (0.0%)
Norway Government Bond,
1.38%, 8/19/30 (b)	NOK	790		91
Poland (0.1%)
Republic of Poland Government Bond,
2.50%, 7/25/27	PLN	820		233
Portugal (0.1%)
Portugal Obrigacoes do Tesouro OT,
0.70%, 10/15/27 (b)	EUR	390		480
Russia (0.1%)
Russian Federal Bond — OFZ,
7.95%, 10/7/26	RUB	21,000		302
Spain (0.7%)
Spain Government Bond,
1.25%, 10/31/30(b)	EUR	1,490		1,921
2.70%, 10/31/48 (b)		300		497
3.45%, 7/30/66 (b)		80		163
				2,581
Supernational (1.0%)
European Investment Bank,
0.20%, 7/15/24		690		835
International Bank for Reconstruction & Development,
SOFR + 0.43%, 0.51%, 8/19/27 (c)	AUD	1,170		1,168
2.20%, 2/27/24		2,190		1,662
				3,665

The accompanying notes are an integral part of the consolidated financial statements.
13

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

	Face Amount (000)		Value (000)
Sweden (0.1%)
Sweden Government Bond,
0.75%, 5/12/28	SEK	1,590	$	190
1.00%, 11/12/26		1,350		163
				353
United Kingdom (1.4%)
United Kingdom Gilt,
0.63%, 10/22/50	GBP	900		1,115
1.63%, 10/22/28		1,000		1,450
3.50%, 1/22/45		820		1,702
4.25%, 9/7/39		450		953
				5,220
				83,364
U.S. Treasury Securities (2.0%)
United States (2.0%)
U.S. Treasury Bonds,
1.13%, 5/15/40	$	2,740		2,703
1.25%, 5/15/50		690		656
2.50%, 2/15/45		1,180		1,456
3.13%, 5/15/48		2,000		2,788
				7,603
Total Fixed Income Securities (Cost $142,514)				151,870
	Shares
Common Stocks (45.6%)
Australia (1.4%)
AGL Energy Ltd.		3,105		30
Alumina Ltd.		11,583		12
Amcor PLC CDI		5,265		58
AMP Ltd.		13,865		13
Ampol Ltd.		1,264		22
APA Group		5,005		37
Aristocrat Leisure Ltd.		2,418		53
ASX Ltd.		868		51
Aurizon Holdings Ltd.		9,285		29
AusNet Services		9,851		13
Australia & New Zealand Banking Group Ltd.		15,161		189
Bank of Queensland Ltd.		2,383		10
Bendigo & Adelaide Bank Ltd.		2,958		13
BHP Group Ltd.		53,401		1,380
Boral Ltd.		5,651		19
Brambles Ltd.		7,217		55
Challenger Ltd.		3,033		8
CIMIC Group Ltd. (f)		518		7
Coca-Cola Amatil Ltd.		2,891		20
Cochlear Ltd.		257		37
Coles Group Ltd.		5,061		62
Commonwealth Bank of Australia		7,509		346
Computershare Ltd.		2,205		20
Crown Resorts Ltd.		1,777		11
CSL Ltd.		1,929		398
Dexus REIT		4,383		28

	Shares		Value (000)
Domino's Pizza Enterprises Ltd.		310	$	18
Flight Centre Travel Group Ltd. (f)		309		3
Fortescue Metals Group Ltd.		32,294		379
Goodman Group REIT		8,162		106
GPT Group (The) REIT		8,494		24
Harvey Norman Holdings Ltd.		2,912		9
Incitec Pivot Ltd.		8,227		12
Insurance Australia Group Ltd.		10,672		34
James Hardie Industries PLC CDI		2,025		49
Lend Lease Group REIT		2,601		21
Macquarie Group Ltd.		1,407		122
Medibank Pvt Ltd.		12,422		22
Mirvac Group REIT		16,831		26
National Australia Bank Ltd.		14,203		182
Newcrest Mining Ltd.		3,382		77
Oil Search Ltd.		6,410		12
OneMarket Ltd. (f)		390		—
Orica Ltd.		1,765		20
Origin Energy Ltd.		7,892		24
Qantas Airways Ltd. (f)		1,836		5
QBE Insurance Group Ltd.		7,227		45
Ramsay Health Care Ltd.		626		30
REA Group Ltd.		267		21
Rio Tinto Ltd.		1,881		128
Santos Ltd.		8,312		29
Scentre Group REIT		24,135		38
Seek Ltd.		1,574		24
Shopping Centres Australasia Property Group REIT		60		—	@
Sonic Healthcare Ltd.		1,897		45
South32 Ltd.		23,497		35
Stockland REIT		12,198		33
Suncorp Group Ltd.		5,829		36
Sydney Airport		5,187		22
Tabcorp Holdings Ltd.		9,164		22
Telstra Corp., Ltd.		19,211		38
TPG Telecom Ltd. (f)		1,809		10
Transurban Group		9,194		94
Treasury Wine Estates Ltd.		3,452		22
Tuas Ltd. (f)		904		—	@
Vicinity Centres REIT		15,698		16
Vocus Group Ltd. (f)		2,924		8
Wesfarmers Ltd.		5,061		162
Westpac Banking Corp.		15,168		184
Woodside Petroleum Ltd.		3,690		47
Woolworths Group Ltd.		5,985		157
				5,312
Austria (0.0%)
IMMOFINANZ AG (f)		332		5
voestalpine AG		1,205		32
				37

The accompanying notes are an integral part of the consolidated financial statements.
14

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

	Shares		Value (000)
Belgium (0.1%)
Ageas		751	$	31
Anheuser-Busch InBev SA N.V.		3,075		166
Colruyt SA		239		15
Groupe Bruxelles Lambert SA		320		29
KBC Group N.V.		1,004		50
Proximus SADP		606		11
Solvay SA		296		25
Telenet Group Holding N.V.		212		8
UCB SA		499		57
Umicore SA		746		31
				423
Brazil (0.1%)
Vale SA		43,500		458
Canada (1.7%)
Agnico Eagle Mines Ltd.		1,200		96
Alimentation Couche-Tard, Inc., Class B		4,262		148
AltaGas Ltd.		1,100		13
ARC Resources Ltd.		1,445		6
Atco Ltd., Class I		600		17
Bank of Montreal		3,398		199
Bank of Nova Scotia (The)		5,711		237
Barrick Gold Corp. (NYSE)		3,432		96
Barrick Gold Corp. (LSE)		4,090		114
Bausch Health Cos., Inc. (f)		1,400		22
BCE, Inc.		1,100		46
Blackberry Ltd. (f)		2,420		11
Bombardier, Inc., Class B (f)		9,698		2
Brookfield Asset Management, Inc., Class A		5,819		193
CAE, Inc.		1,300		19
Cameco Corp.		1,934		20
Canadian Imperial Bank of Commerce		1,738		130
Canadian National Railway Co.		3,676		391
Canadian Natural Resources Ltd.		5,229		84
Canadian Pacific Railway Ltd.		1,100		335
Canadian Tire Corp., Ltd., Class A		600		60
Canadian Utilities Ltd., Class A		1,000		24
CCL Industries, Inc., Class B		1,200		46
Cenovus Energy, Inc.		3,569		14
CGI, Inc. (f)		1,200		81
CI Financial Corp.		1,200		15
Constellation Software, Inc.		100		111
Crescent Point Energy Corp.		2,613		3
Dollarama, Inc.		2,000		77
Eldorado Gold Corp. (f)		738		8
Element Fleet Management Corp.		1,938		16
Emera, Inc.		500		21
Empire Co., Ltd., Class A		1,100		32
Enbridge, Inc.		4,747		139
Fairfax Financial Holdings Ltd.		100		29
Finning International, Inc.		1,100		17
First Quantum Minerals Ltd.		3,394		30
Fortis, Inc.		1,934		79

	Shares		Value (000)
Franco-Nevada Corp.		1,100	$	154
George Weston Ltd.		631		46
Gildan Activewear, Inc.		1,300		26
Great-West Lifeco, Inc.		1,300		25
H&R Real Estate Investment Trust REIT		1,100		8
Husky Energy, Inc.		1,698		4
Hydro One Ltd.		1,200		25
IA Financial Corp., Inc.		800		28
IGM Financial, Inc.		700		16
Imperial Oil Ltd.		1,256		15
Intact Financial Corp.		1,000		107
Inter Pipeline Ltd.		1,545		15
Keyera Corp.		1,200		18
Kinross Gold Corp. (f)		5,514		49
Linamar Corp.		500		15
Loblaw Cos., Ltd.		1,373		72
Magna International, Inc.		6,210		284
Manulife Financial Corp.		9,483		132
Methanex Corp.		700		17
Metro, Inc.		1,200		58
National Bank of Canada		1,400		70
Nutrien Ltd.		3,369		132
Onex Corp.		700		31
Open Text Corp.		1,200		51
Pembina Pipeline Corp.		2,558		54
Peyto Exploration & Development Corp.		1,200		2
Power Corp. of Canada		3,012		59
PrairieSky Royalty Ltd.		977		6
Restaurant Brands International, Inc.		1,200		69
RioCan Real Estate Investment Trust REIT		1,100		12
Rogers Communications, Inc., Class B		1,442		57
Royal Bank of Canada		6,967		489
Saputo, Inc.		1,400		35
Seven Generations Energy Ltd., Class A (f)		1,600		4
Shaw Communications, Inc., Class B		1,934		35
SmartCentres Real Estate Investment Trust REIT		600		9
SNC-Lavalin Group, Inc.		1,100		18
Sun Life Financial, Inc.		2,905		118
Suncor Energy, Inc.		8,088		99
TC Energy Corp.		4,062		171
Teck Resources Ltd., Class B		3,009		42
TELUS Corp.		2,100		37
Thomson Reuters Corp.		1,389		111
Toronto-Dominion Bank (The)		8,709		403
Tourmaline Oil Corp.		1,200		15
Trisura Group Ltd. (f)		27		2
Turquoise Hill Resources Ltd. (f)		5,340		5
Vermilion Energy, Inc.		800		2
West Fraser Timber Co., Ltd.		600		28
Wheaton Precious Metals Corp.		2,031		100
Yamana Gold, Inc.		3,962		22
				6,383

The accompanying notes are an integral part of the consolidated financial statements.
15

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

	Shares		Value (000)
China (0.2%)
BAIC Motor Corp., Ltd. H Shares (g)		24,336	$	10
Brilliance China Automotive Holdings Ltd. (g)		42,831		41
BYD Co., Ltd. H Shares (f)		9,734		157
China Common Rich Renewable Energy Investments Ltd. (f)		42,000		—
Dongfeng Motor Group Co., Ltd. H Shares (g)		35,043		22
Fuyao Glass Industry Group Co. Ltd. (g)		7,787		29
Geely Automobile Holdings Ltd. (g)		91,449		183
Great Wall Motor Co., Ltd. H Shares (g)		48,645		62
Guangzhou Automobile Group Co., Ltd. H Shares (g)		42,831		36
NIO, Inc. ADR (f)		12,065		256
Wharf Holdings Ltd. (The) (g)		13,200		26
				822
Denmark (0.4%)
AP Moller — Maersk A/S Series A		14		21
AP Moller — Maersk A/S Series B		29		46
Carlsberg A/S Series B		55		7
Coloplast A/S Series B		66		10
Danske Bank A/S (f)		3,140		42
Drilling Co of 1972 A/S/The (f)		104		2
DSV A/S		1,791		291
Novo Nordisk A/S Series B		10,114		701
Novozymes A/S Series B		1,439		90
Vestas Wind Systems A/S		1,810		293
				1,503
Finland (0.3%)
Elisa Oyj		601		35
Fortum Oyj		1,836		37
Kone Oyj, Class B		1,416		124
Metso Outotec Oyj		2,033		14
Neles Oyj		473		6
Neste Oyj		1,646		87
Nokia Oyj (f)		24,585		96
Nokian Renkaat Oyj		10,529		298
Nordea Bank Abp (f) (OMXH)		194		2
Nordea Bank Abp (f) (SSE)		14,028		107
Orion Oyj, Class B		439		20
Sampo Oyj, Class A		1,873		74
Stora Enso Oyj, Class R		2,345		37
UPM-Kymmene Oyj		2,245		68
Wartsila Oyj Abp		1,880		15
				1,020
France (2.2%)
Accor SA (f)		16,287		456
Aeroports de Paris (ADP)		122		12
Air Liquide SA		1,936		307
Airbus SE (f)		2,412		175
Alstom SA (f)		631		31
Amundi SA (f)		245		17
ArcelorMittal (f)		2,718		36

	Shares		Value (000)
Arkema SA		279	$	30
Atos SE (f)		393		32
AXA SA		7,969		147
BioMerieux		172		27
BNP Paribas SA (f)		4,613		167
Bollore SA		3,563		13
Bouygues SA		876		30
Bureau Veritas SA (f)		1,088		25
Capgemini SE		660		85
Carrefour SA		2,338		37
Casino Guichard Perrachon SA (f)		226		5
Cie de Saint-Gobain (f)		2,095		88
Cie Generale des Etablissements Michelin SCA		16,395		1,760
CNP Assurances (f)		694		9
Covivio REIT		137		10
Credit Agricole SA (f)		4,654		41
Danone SA		2,491		161
Dassault Aviation SA (f)		11		9
Dassault Systemes SE		537		100
Edenred		915		41
Eiffage SA (f)		301		25
Electricite de France SA		2,348		25
Engie SA (f)		7,578		101
EssilorLuxottica SA (f)		851		116
Eurazeo SE (f)		194		10
Eurofins Scientific SE (f)		46		36
Eutelsat Communications SA		722		7
Faurecia SE (f)		1,443		62
Gecina SA REIT		195		26
Getlink SE (f)		1,904		26
Hermes International		130		112
ICADE REIT		137		8
Iliad SA		107		20
Imerys SA		153		6
Ingenico Group SA (f)		243		38
Ipsen SA		155		16
JCDecaux SA (f)		304		5
Kering SA		313		208
Klepierre SA REIT		902		13
L'Oreal SA (BSRM)		1,040		338
Lagardere SCA (f)		490		12
Legrand SA		1,087		87
LVMH Moet Hennessy Louis Vuitton SE		1,154		540
Natixis SA (f)		3,881		9
Orange SA		8,178		85
Pernod Ricard SA		887		141
Peugeot SA (f)		11,226		204
Publicis Groupe SA		854		28
Remy Cointreau SA		95		17
Renault SA (f)		787		20
Rexel SA (f)		1,228		15
Safran SA (f)		1,368		135
Sanofi		4,584		459

The accompanying notes are an integral part of the consolidated financial statements.
16

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

	Shares		Value (000)
France (cont'd)
Schneider Electric SE		2,332	$	290
SCOR SE (f)		706		20
SEB SA		94		15
SES SA		1,501		11
Societe BIC SA		117		6
Societe Generale SA (f)		3,139		42
Sodexo SA		378		27
STMicroelectronics N.V.		2,775		85
Suez		1,805		33
Teleperformance		239		74	��
Thales SA		439		33
TOTAL SA		9,675		332
Ubisoft Entertainment SA (f)		260		23
Unibail-Rodamco-Westfield REIT		408		15
Unibail-Rodamco-Westfield REIT CDI		2,974		5
Valeo SA		4,424		136
Veolia Environnement SA		2,032		44
Vinci SA		2,076		173
Vivendi SA		4,239		118
Wendel SA		115		10
Worldline SA (f)		156		13
				8,306
Germany (1.9%)
1&1 Drillisch AG		229		5
Adidas AG (f)		769		248
Allianz SE (Registered)		1,840		353
BASF SE		3,783		230
Bayer AG (Registered)		3,413		211
Bayerische Motoren Werke AG		6,488		471
Bayerische Motoren Werke AG (Preference)		1,086		59
Beiersdorf AG		416		47
Brenntag AG		639		41
Commerzbank AG (f)		4,353		21
Continental AG		2,116		229
Covestro AG		662		33
Daimler AG (Registered)		17,105		923
Deutsche Bank AG (Registered) (f)		8,417		71
Deutsche Boerse AG		772		135
Deutsche Lufthansa AG (Registered) (f)		974		8
Deutsche Post AG (Registered)		3,982		181
Deutsche Telekom AG (Registered)		13,693		228
Deutsche Wohnen SE		1,453		73
E.ON SE		9,245		102
Evonik Industries AG		668		17
Fraport AG Frankfurt Airport Services Worldwide (f)		171		7
Fresenius Medical Care AG & Co., KGaA		888		75
Fresenius SE & Co., KGaA		1,711		78
Fuchs Petrolub SE (Preference)		287		15
GEA Group AG		721		25
Hannover Rueck SE (Registered)		245		38
HeidelbergCement AG		623		38

	Shares		Value (000)
Henkel AG & Co., KGaA		429	$	40
Henkel AG & Co., KGaA (Preference)		738		77
Hochtief AG		79		6
Hugo Boss AG		264		7
Infineon Technologies AG		4,808		136
K+S AG (Registered)		780		5
KION Group AG		294		25
LANXESS AG		377		22
Linde PLC (f)		1,188		281
Merck KGaA		531		77
METRO AG		736		7
MTU Aero Engines AG		213		35
Muenchener Rueckversicherungs-Gesellschaft AG in Muenchen (Registered)		636		162
OSRAM Licht AG (f)		408		24
Porsche Automobil Holding SE (Preference) (f)		3,000		179
ProSiebenSat.1 Media SE (Registered) (f)		968		13
Puma SE (f)		261		24
QIAGEN N.V. (f)		896		47
RTL Group SA (f)		159		6
RWE AG		2,186		82
SAP SE		4,031		628
Schaeffler AG (Preference)		1,000		6
Siemens AG (Registered)		3,170		400
Symrise AG		512		71
Telefonica Deutschland Holding AG		3,079		8
thyssenKrupp AG (f)		1,787		9
Uniper SE		829		27
United Internet AG (Registered)		503		19
Volkswagen AG (f)		592		104
Volkswagen AG (Preference) (f)		3,582		576
Vonovia SE		2,015		138
Wirecard AG (f)		496		—	@
Zalando SE (f)		465		43
				7,246
Greece (0.0%)
National Bank of Greece SA (f)		9		—	@
Hong Kong (0.5%)
AIA Group Ltd.		52,200		519
ASM Pacific Technology Ltd.		1,000		10
Bank of East Asia Ltd. (The)		6,994		13
BOC Hong Kong Holdings Ltd.		18,500		49
Cathay Pacific Airways Ltd. (f)		5,000		3
CK Asset Holdings Ltd.		12,364		61
CK Hutchison Holdings Ltd.		11,364		69
CK Infrastructure Holdings Ltd.		4,000		19
CLP Holdings Ltd.		7,500		70
First Pacific Co., Ltd.		10,000		3
Galaxy Entertainment Group Ltd.		10,000		68
Hang Lung Group Ltd.		5,000		11
Hang Lung Properties Ltd.		10,000		25
Hang Seng Bank Ltd.		3,800		56
Henderson Land Development Co., Ltd.		7,644		28

The accompanying notes are an integral part of the consolidated financial statements.
17

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

	Shares		Value (000)
Hong Kong (cont'd)
HK Electric Investments & HK Electric Investments Ltd.		12,500	$	13
HKT Trust & HKT Ltd.		11,000		15
Hong Kong & China Gas Co., Ltd.		51,561		75
Hong Kong Exchanges & Clearing Ltd.		5,440		256
Hongkong Land Holdings Ltd.		5,600		21
Hysan Development Co., Ltd.		4,000		12
I-CABLE Communications Ltd. (f)		7,559		—	@
Jardine Matheson Holdings Ltd.		1,000		40
Kerry Properties Ltd.		3,500		9
Link REIT		9,882		81
Melco Resorts & Entertainment Ltd. ADR		900		15
MGM China Holdings Ltd.		3,600		4
MTR Corp., Ltd.		7,392		37
New World Development Co. Ltd.		7,841		38
NWS Holdings Ltd.		8,000		6
Pacific Century Premium Developments Ltd. (f)		2,160		1
PCCW Ltd.		21,000		13
Power Assets Holdings Ltd.		6,500		34
Sands China Ltd.		11,600		45
Shangri-La Asia Ltd. (f)		8,000		6
Sino Land Co., Ltd.		17,725		21
SJM Holdings Ltd.		9,000		11
Sun Hung Kai Properties Ltd.		7,004		90
Swire Pacific Ltd., Class A		2,000		10
Swire Properties Ltd.		5,550		15
Techtronic Industries Co., Ltd.		6,500		86
WH Group Ltd.		39,500		32
Wharf Real Estate Investment Co., Ltd.		12,200		50
Wynn Macau Ltd. (f)		8,000		13
Yue Yuen Industrial Holdings Ltd.		4,000		6
				2,059
Ireland (0.1%)
AIB Group PLC (f)		3,316		3
Bank of Ireland Group PLC (f)		3,768		7
CRH PLC		3,431		124
Flutter Entertainment PLC (f)		332		53
Kerry Group PLC, Class A		645		83
				270
Italy (0.5%)
Assicurazioni Generali SpA		5,058		71
Atlantia SpA (f)		1,869		29
CNH Industrial N.V. (f)		4,274		33
Davide Campari-Milano		2,426		26
Enel SpA		33,642		292
Eni SpA		10,436		81
EXOR N.V.		444		24
Ferrari N.V.		2,394		439
Fiat Chrysler Automobiles N.V. (f)		21,806		268
Intesa Sanpaolo SpA (f)		55,945		105
Leonardo SpA		1,685		10

	Shares		Value (000)
Mediobanca Banca di Credito Finanziario SpA		2,344	$	18
Pirelli & C SpA (f)		79,275		340
Poste Italiane SpA		2,151		19
Prysmian SpA		852		25
Recordati SpA		449		23
Snam SpA		9,450		49
Telecom Italia SpA		71,769		29
Tenaris SA		1,951		10
Terna Rete Elettrica Nazionale SpA		5,867		41
UniCredit SpA (f)		8,182		68
UnipolSai Assicurazioni SpA		4,062		11
				2,011
Japan (1.8%)
Aisin Seiki Co., Ltd.		2,726		87
Bridgestone Corp.		60,061		1,899
Denso Corp.		6,909		303
Honda Motor Co., Ltd.		25,588		608
Isuzu Motors Ltd.		9,145		80
JTEKT Corp.		2,820		22
Koito Manufacturing Co., Ltd.		1,752		89
Mazda Motor Corp.		8,756		51
Mitsubishi Motors Corp. (f)		8,756		19
NGK Spark Plug Co., Ltd.		2,336		41
Nissan Motor Co., Ltd. (f)		37,848		134
Stanley Electric Co., Ltd.		1,947		56
Subaru Corp.		9,729		189
Sumitomo Electric Industries Ltd.		11,676		131
Sumitomo Rubber Industries Ltd.		21,831		203
Toyo Tire Corp.		11,400		185
Toyoda Gosei Co., Ltd.		1,168		27
Toyota Industries Corp.		2,531		160
Toyota Motor Corp.		33,275		2,208
Yamaha Motor Co., Ltd.		4,378		64
Yokohama Rubber Co., Ltd. (The)		13,857		197
				6,753
Netherlands (0.6%)
ABN Amro Bank N.V. CVA		1,755		15
Aegon N.V.		7,272		19
AerCap Holdings N.V. (f)		600		15
Akzo Nobel N.V.		923		93
Altice Europe N.V. (f)		2,239		11
ASML Holding N.V.		1,629		602
Basic-Fit N.V. (f)		3,193		76
Boskalis Westminster (f)		373		8
Coca-Cola European Partners PLC		900		35
Heineken Holding N.V.		475		37
Heineken N.V.		1,070		95
ING Groep N.V. (f)		16,088		115
Koninklijke Ahold Delhaize N.V.		5,421		160
Koninklijke DSM N.V.		746		123
Koninklijke KPN N.V.		14,131		33
Koninklijke Philips N.V. (f)		3,947		186

The accompanying notes are an integral part of the consolidated financial statements.
18

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

	Shares		Value (000)
Netherlands (cont'd)
Koninklijke Vopak N.V.		288	$	16
NN Group N.V.		1,251		47
Randstad N.V. (f)		485		25
Unilever N.V.		6,720		408
Wolters Kluwer N.V.		1,242		106
				2,225
New Zealand (0.1%)
Auckland International Airport Ltd. (f)		8,426		41
Contact Energy Ltd.		6,107		27
Fletcher Building Ltd. (f)		5,762		15
Mercury NZ Ltd.		5,917		20
Meridian Energy Ltd.		10,965		36
Ryman Healthcare Ltd.		3,227		30
Spark New Zealand Ltd.		15,294		48
				217
Norway (0.1%)
Akastor ASA (f)		892		1
Aker Carbon Capture AS (f)		669		—	@
Aker Offshore Wind Holding AS (f)		669		—	@
Aker Solutions ASA (f)		892		1
DNB ASA (f)		4,504		63
Equinor ASA		5,009		71
Kvaerner ASA (f)		816		1
Norsk Hydro ASA (f)		5,242		14
Orkla ASA		3,898		39
REC Silicon ASA (f)		649		—	@
Seadrill Ltd. (f)		1		—	@
Subsea 7 SA (f)		1,189		9
Telenor ASA		6,190		104
Yara International ASA		776		30
				333
Poland (0.0%)
Jeronimo Martins SGPS SA		2,786		45
Portugal (0.0%)
Galp Energia SGPS SA		2,600		24
Pharol SGPS SA (Registered) (f)		11,120		2
				26
South Africa (0.0%)
Nedbank Group Ltd.		633		4
Old Mutual Ltd.		19,716		12
				16
Spain (0.3%)
ACS Actividades de Construccion y Servicios SA		1,049		24
Aena SME SA (f)		277		38
Amadeus IT Group SA		1,807		100
Banco Bilbao Vizcaya Argentaria SA		27,331		76
Banco de Sabadell SA		22,275		8
Banco Santander SA (f)		66,432		124
Bankia SA		4,118		6
Bankinter SA		2,774		12
CaixaBank SA		14,871		32

	Shares		Value (000)
Enagas SA		939	$	22
Endesa SA		1,308		35
Ferrovial SA		2,034		49
Grifols SA		1,228		35
Iberdrola SA		23,703		292
Industria de Diseno Textil SA		4,465		123
International Consolidated Airlines Group SA		2,565		3
Mapfre SA		4,445		7
Melia Hotels International SA (f)		14,735		54
Naturgy Energy Group SA		1,452		29
Red Electrica Corp., SA		1,793		34
Repsol SA		5,281		36
Siemens Gamesa Renewable Energy SA		1,000		27
Telefonica SA		18,669		64
Telepizza Group SA (f)		156		1
				1,231
Sweden (0.5%)
Alfa Laval AB (f)		1,371		30
Assa Abloy AB, Class B		4,670		109
Atlas Copco AB, Class A		3,100		148
Atlas Copco AB, Class B		1,804		75
Boliden AB		1,251		37
Electrolux AB, Class B		1,108		26
Electrolux Professional AB (f)		1,099		4
Epiroc AB, Class A		3,100		45
Epiroc AB, Class B		1,919		27
Essity AB, Class B (f)		2,848		96
Getinge AB, Class B		1,110		24
Hennes & Mauritz AB, Class B		4,306		74
Hexagon AB, Class B (f)		1,192		90
Husqvarna AB, Class B		1,961		22
ICA Gruppen AB		390		20
Industrivarden AB, Class C (f)		834		22
Investor AB, Class B		2,152		141
Kinnevik AB		1,152		47
L E Lundbergforetagen AB, Class B (f)		382		19
Lundin Energy AB		864		17
Millicom International Cellular SA SDR		327		10
Modern Times Group MTG AB, Class B (f)		44		1
Nordic Entertainment Group AB, Class B (f)		44		2
Sandvik AB (f)		5,141		101
Securitas AB, Class B (f)		1,445		22
Skandinaviska Enskilda Banken AB, Class A (f)		7,057		63
Skanska AB, Class B (f)		1,569		33
SKF AB, Class B		1,759		36
Svenska Handelsbanken AB, Class A (f)		6,968		58
Swedbank AB, Class A (f)		4,171		65
Swedish Match AB		836		68
Tele2 AB, Class B		1,653		23
Telefonaktiebolaget LM Ericsson, Class B		14,612		160
Telia Co., AB		11,968		49
Volvo AB, Class B (f)		7,191		138
				1,902

The accompanying notes are an integral part of the consolidated financial statements.
19

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

	Shares		Value (000)
Switzerland (1.7%)
ABB Ltd. (Registered)		15,641	$	398
Adecco Group AG (Registered)		627		33
Alcon, Inc. (f)		1,967		111
Cie Financiere Richemont SA (Registered)		2,222		149
Credit Suisse Group AG (Registered)		7,378		74
Geberit AG (Registered)		375		222
Givaudan SA (Registered)		44		190
Idorsia Ltd. (f)		503		13
Julius Baer Group Ltd.		1,051		45
Kuehne & Nagel International AG (Registered)		337		65
LafargeHolcim Ltd. (Registered) (f) (Euronext)		1,910		87
LafargeHolcim Ltd. (Registered) (f) (SIX)		166		8
Lonza Group AG (Registered)		235		145
Nestle SA (Registered)		16,332		1,944
Novartis AG (Registered)		10,107		877
Roche Holding AG (Genusschein)		2,751		942
SGS SA (Registered)		26		70
Siemens Energy AG (f)		1,585		43
Sonova Holding AG (Registered) (f)		435		110
Swatch Group AG (The)		159		37
Swiss Re AG		615		46
Swisscom AG (Registered)		311		165
Transocean Ltd. (f)		1,913		2
UBS Group AG (Registered)		12,706		142
Zurich Insurance Group AG		1,085		378
				6,296
United Kingdom (2.6%)
3i Group PLC		4,619		59
Admiral Group PLC		956		32
Anglo American PLC		5,995		145
Antofagasta PLC		1,915		25
Ashtead Group PLC		2,395		86
Associated British Foods PLC		1,697		41
AstraZeneca PLC		5,702		623
Auto Trader Group PLC		4,887		36
Aviva PLC		19,475		72
Babcock International Group PLC		1,273		4
BAE Systems PLC		15,137		94
Barclays PLC (f)		76,403		96
Barratt Developments PLC		4,717		29
Berkeley Group Holdings PLC		608		33
BHP Group PLC		9,893		211
BP PLC		87,860		254
British American Tobacco PLC		10,120		363
British Land Co., PLC (The) REIT		4,658		20
BT Group PLC		40,614		51
Bunzl PLC		1,590		51
Burberry Group PLC		2,099		42
Capita PLC (f)		3,863		2
Carnival PLC		906		12
Centrica PLC		25,312		13

	Shares		Value (000)
Coca-Cola HBC AG (f)		913	$	23
Compass Group PLC		7,054		106
ConvaTec Group PLC		6,675		15
Croda International PLC		608		49
DCC PLC		425		33
Diageo PLC		11,181		384
Direct Line Insurance Group PLC		6,389		22
Dixons Carphone PLC		5,049		6
easyJet PLC		789		5
Experian PLC		4,522		170
Ferguson PLC		1,176		118
Fresnillo PLC		1,140		18
G4S PLC (f)		6,550		17
GlaxoSmithKline PLC		22,079		414
Glencore PLC (f)		55,105		114
Hammerson PLC REIT (f)		793		—	@
Hargreaves Lansdown PLC		1,243		25
Hikma Pharmaceuticals PLC		684		23
HSBC Holdings PLC		90,206		353
IMI PLC		1,324		18
Imperial Brands PLC		4,161		74
InterContinental Hotels Group PLC (f)		10,109		531
Intertek Group PLC		781		64
Intu Properties PLC REIT (f)		5,299		—	@
Investec PLC		3,345		6
ITV PLC		17,090		15
J Sainsbury PLC		7,901		20
Johnson Matthey PLC		911		28
Kingfisher PLC		10,186		39
Land Securities Group PLC REIT		3,515		24
Legal & General Group PLC		28,615		70
Lloyds Banking Group PLC (f)		321,808		109
London Stock Exchange Group PLC		1,537		176
M&G PLC		11,531		24
Marks & Spencer Group PLC		8,120		10
Mediclinic International PLC		1,879		7
Meggitt PLC		3,776		13
Melrose Industries PLC (f)		17,615		26
Micro Focus International PLC (f)		1,468		5
Mondi PLC		1,740		37
National Grid PLC		15,212		175
Next PLC		680		52
Ninety One PLC (f)		1,672		4
Paragon Offshore PLC (f)(h)		303		—
Pearson PLC		3,983		28
Persimmon PLC		1,445		46
Provident Financial PLC (f)		917		2
Prudential PLC		11,586		166
Quilter PLC		7,967		13
Reckitt Benckiser Group PLC		3,018		294
RELX PLC (Euronext N.V.)		4,935		110
RELX PLC (LSE)		5,143		115
Rio Tinto PLC		19,351		1,164

The accompanying notes are an integral part of the consolidated financial statements.
20

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

	Shares		Value (000)
United Kingdom (cont'd)
Rolls-Royce Holdings PLC		7,917	$	13
Royal Bank of Scotland Group PLC (f)		17,032		23
Royal Dutch Shell PLC, Class A		20,099		251
Royal Dutch Shell PLC, Class B		16,836		204
Royal Mail PLC		4,551		14
RSA Insurance Group PLC		4,901		29
Sage Group PLC (The)		5,214		49
Schroders PLC		603		21
Segro PLC REIT		4,773		57
Severn Trent PLC		1,169		37
Smith & Nephew PLC		4,215		83
Smiths Group PLC		1,878		33
SSE PLC		4,827		75
St. James's Place PLC		2,509		30
Standard Chartered PLC (f)		15,915		73
Standard Life Aberdeen PLC		11,117		32
Tate & Lyle PLC		2,231		19
Taylor Wimpey PLC		15,388		22
Tesco PLC		40,719		112
Travis Perkins PLC		1,211		17
TUI AG		2,220		8
Unilever PLC		5,697		351
United Utilities Group PLC		3,244		36
Vodafone Group PLC		119,724		159
Weir Group PLC (The)		1,065		17
Whitbread PLC (f)		9,590		262
Wm Morrison Supermarkets PLC		10,067		22
WPP PLC		6,145		48
				9,851
United States (28.5%)
3M Co.		5,110		819
Abbott Laboratories		4,134		450
AbbVie, Inc.		4,194		367
ABIOMED, Inc. (f)		164		45
Accenture PLC, Class A		1,455		329
Activision Blizzard, Inc.		1,693		137
Acuity Brands, Inc.		238		24
Adobe, Inc. (f)		1,227		602
Advance Auto Parts, Inc.		249		38
Advanced Micro Devices, Inc. (f)		2,301		189
AES Corp.		2,045		37
Affiliated Managers Group, Inc.		283		19
Aflac, Inc.		1,834		67
Agilent Technologies, Inc.		817		82
AGNC Investment Corp. REIT		1,484		21
Air Products & Chemicals, Inc.		579		172
Akamai Technologies, Inc. (f)		476		53
Albemarle Corp.		264		24
Alexandria Real Estate Equities, Inc. REIT		197		32
Alexion Pharmaceuticals, Inc. (f)		496		57
Align Technology, Inc. (f)		170		56

	Shares		Value (000)
Alkermes PLC (f)		449	$	7
Alleghany Corp.		51		27
Allegion PLC		822		81
Alliance Data Systems Corp.		268		11
Alliant Energy Corp.		540		28
Allstate Corp. (The)		869		82
Ally Financial, Inc.		1,301		33
Alnylam Pharmaceuticals, Inc. (f)		243		35
Alphabet, Inc., Class A (f)		659		966
Alphabet, Inc., Class C (f)		813		1,195
Altice USA, Inc., Class A (f)		1,477		38
Altria Group, Inc.		4,325		167
Amazon.com, Inc. (f)		1,068		3,363
Amcor PLC		3,738		41
AMERCO		63		22
Ameren Corp.		569		45
American Airlines Group, Inc.		292		4
American Electric Power Co., Inc.		1,253		102
American Express Co.		1,633		164
American Financial Group, Inc.		267		18
American International Group, Inc.		2,047		56
American Tower Corp. REIT		1,064		257
American Water Works Co., Inc.		443		64
Ameriprise Financial, Inc.		278		43
AmerisourceBergen Corp.		458		44
AMETEK, Inc.		1,914		190
Amgen, Inc.		1,433		364
Amphenol Corp., Class A		640		69
Analog Devices, Inc.		987		115
Annaly Capital Management, Inc. REIT		4,134		29
ANSYS, Inc. (f)		196		64
Anthem, Inc.		584		157
AO Smith Corp.		1,315		69
Aon PLC		546		113
Apache Corp.		1,119		11
Apple, Inc.		43,128		4,995
Applied Materials, Inc.		2,190		130
Aptiv PLC		4,774		438
Aramark		768		20
Arch Capital Group Ltd. (f)		1,319		39
Archer-Daniels-Midland Co.		1,259		59
Arconic Corp. (f)		357		7
Arista Networks, Inc. (f)		185		38
Arrow Electronics, Inc. (f)		293		23
Arthur J Gallagher & Co.		550		58
Assurant, Inc.		217		26
AT&T, Inc.		16,732		477
Athene Holding Ltd., Class A (f)		470		16
Atmos Energy Corp.		215		21
Autodesk, Inc. (f)		579		134
Autoliv, Inc.		1,452		106
Automatic Data Processing, Inc.		1,047		146
AutoZone, Inc. (f)		87		102

The accompanying notes are an integral part of the consolidated financial statements.
21

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

	Shares		Value (000)
United States (cont'd)
AvalonBay Communities, Inc. REIT		389	$	58
Avery Dennison Corp.		202		26
Axalta Coating Systems Ltd. (f)		738		16
Baker Hughes Co.		1,508		20
Ball Corp.		841		70
Bank of America Corp.		21,264		512
Bank of New York Mellon Corp. (The)		2,049		70
Baxter International, Inc.		1,230		99
Becton Dickinson & Co.		559		130
Berkshire Hathaway, Inc., Class B (f)		2,908		619
Best Buy Co., Inc.		539		60
Biogen, Inc. (f)		493		140
BioMarin Pharmaceutical, Inc. (f)		528		40
BlackRock, Inc.		220		124
Boeing Co. (The)		4,663		771
Booking Holdings, Inc. (f)		158		270
BorgWarner, Inc.		3,728		144
Boston Properties, Inc. REIT		545		44
Boston Scientific Corp. (f)		3,263		125
Brighthouse Financial, Inc. (f)		268		7
Bristol-Myers Squibb Co.		5,422		327
Broadcom, Inc.		873		318
Broadridge Financial Solutions, Inc.		207		27
Brown-Forman Corp., Class B		787		59
Bunge Ltd.		493		23
Burlington Stores, Inc. (f)		232		48
Cabot Oil & Gas Corp.		1,385		24
Cadence Design Systems, Inc. (f)		600		64
Camden Property Trust REIT		341		30
Campbell Soup Co.		484		23
Capital One Financial Corp.		1,147		82
Capri Holdings Ltd. (f)		511		9
Cardinal Health, Inc.		654		31
CarMax, Inc. (f)		496		46
Carnival Corp.		1,368		21
Carrier Global Corp.		7,717		236
Caterpillar, Inc.		4,927		735
Cboe Global Markets, Inc.		291		26
CBRE Group, Inc., Class A (f)		1,032		48
CDK Global, Inc.		334		15
CDW Corp.		412		49
Celanese Corp.		241		26
Centene Corp. (f)		1,662		97
CenterPoint Energy, Inc.		1,575		30
CenturyLink, Inc.		2,906		29
Cerner Corp.		849		61
CF Industries Holdings, Inc.		766		24
CH Robinson Worldwide, Inc.		1,194		122
Charles Schwab Corp. (The)		2,768		100
Charter Communications, Inc., Class A (f)		453		283
Chemours Co. (The)		464		10
Cheniere Energy, Inc. (f)		512		24

	Shares		Value (000)
Chevron Corp.		4,373	$	315
Chipotle Mexican Grill, Inc. (f)		92		114
Choice Hotels International, Inc.		2,634		226
Chubb Ltd.		1,120		130
Church & Dwight Co., Inc.		567		53
Cigna Corp.		821		139
Cimarex Energy Co.		254		6
Cincinnati Financial Corp.		447		35
Cintas Corp.		790		263
Cisco Systems, Inc.		10,142		399
CIT Group, Inc.		277		5
Citigroup, Inc.		5,393		232
Citizens Financial Group, Inc.		1,348		34
Citrix Systems, Inc.		260		36
Clorox Co. (The)		246		52
CME Group, Inc.		964		161
CMS Energy Corp.		608		37
Coca-Cola Co. (The)		9,534		471
Cognex Corp.		495		32
Cognizant Technology Solutions Corp., Class A		1,326		92
Colgate-Palmolive Co.		1,880		145
Comcast Corp., Class A		10,430		482
Comerica, Inc.		532		20
CommScope Holding Co., Inc. (f)		568		5
Conagra Brands, Inc.		1,109		40
Concho Resources, Inc.		510		23
ConocoPhillips		2,586		85
Consolidated Edison, Inc.		841		65
Constellation Brands, Inc., Class A		482		91
Continental Resources, Inc.		331		4
Cooper Cos., Inc. (The)		177		60
Cooper Tire & Rubber Co.		3,800		120
Copart, Inc. (f)		1,882		198
Corning, Inc.		1,838		60
Corteva, Inc.		1,710		49
CoStar Group, Inc. (f)		452		384
Costco Wholesale Corp.		1,043		370
Coty, Inc., Class A		960		3
Crown Castle International Corp. REIT		1,081		180
Crown Holdings, Inc. (f)		378		29
CSX Corp.		6,637		515
Cummins, Inc.		1,390		294
CVS Health Corp.		2,939		172
Danaher Corp.		1,463		315
Darden Restaurants, Inc.		329		33
DaVita, Inc. (f)		335		29
Deere & Co.		2,594		575
Dell Technologies, Inc., Class C (f)		441		30
Delta Air Lines, Inc.		1,508		46
DENTSPLY SIRONA, Inc.		780		34
Devon Energy Corp.		1,335		13
DexCom, Inc. (f)		227		94
Diamondback Energy, Inc.		541		16

The accompanying notes are an integral part of the consolidated financial statements.
22

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

	Shares		Value (000)
United States (cont'd)
Digital Realty Trust, Inc. REIT		536	$	79
Discover Financial Services		855		49
Discovery, Inc., Class A (f)		441		10
Discovery, Inc., Class C (f)		1,144		22
DISH Network Corp., Class A (f)		705		20
DocuSign, Inc. (f)		164		35
Dollar General Corp.		523		110
Dollar Tree, Inc. (f)		536		49
Dominion Energy, Inc.		1,933		153
Domino's Pizza, Inc.		236		100
Dover Corp.		1,357		147
Dow, Inc.		1,705		80
DR Horton, Inc.		42,058		3,181
Dropbox, Inc., Class A (f)		571		11
DTE Energy Co.		446		51
Duke Energy Corp.		1,686		149
Duke Realty Corp. REIT		968		36
DuPont de Nemours, Inc.		1,674		93
DXC Technology Co.		728		13
E*Trade Financial Corp.		865		43
Eagle Materials, Inc.		1,057		91
East West Bancorp, Inc.		492		16
Eastman Chemical Co.		377		29
Eaton Corp., PLC		3,658		373
Eaton Vance Corp.		305		12
eBay, Inc.		2,047		107
Ecolab, Inc.		522		104
Edison International		849		43
Edwards Lifesciences Corp. (f)		1,844		147
Elanco Animal Health, Inc. (f)		780		22
Electronic Arts, Inc. (f)		663		86
Eli Lilly & Co.		2,154		319
Emerson Electric Co.		5,338		350
Entergy Corp.		471		46
EOG Resources, Inc.		1,348		48
EPAM Systems, Inc. (f)		192		62
Equifax, Inc.		1,006		158
Equinix, Inc. REIT		185		141
Equitable Holdings, Inc.		831		15
Equity Lifestyle Properties, Inc. REIT		470		29
Equity Residential REIT		1,006		52
Erie Indemnity Co., Class A		90		19
ESC Seventy Seven (f)(h)		275		—
Essex Property Trust, Inc. REIT		232		47
Estee Lauder Cos., Inc. (The), Class A		564		123
Everest Re Group Ltd.		243		48
Evergy, Inc.		600		30
Eversource Energy		825		69
Exact Sciences Corp. (f)		351		36
Exelon Corp.		2,235		80
Expedia Group, Inc.		325		30
Expeditors International of Washington, Inc.		1,531		139

	Shares		Value (000)
Extended Stay America, Inc. (Units) (i)		8,667	$	104
Extra Space Storage, Inc. REIT		249		27
Exxon Mobil Corp.		9,719		334
F5 Networks, Inc. (f)		206		25
Facebook, Inc., Class A (f)		5,617		1,471
Factset Research Systems, Inc.		235		79
Fastenal Co.		4,976		224
Federal Realty Investment Trust REIT		262		19
FedEx Corp.		2,126		535
Fidelity National Financial, Inc.		8,119		254
Fidelity National Information Services, Inc.		1,316		194
Fifth Third Bancorp		1,902		41
First American Financial Corp.		3,114		159
First Republic Bank		456		50
FirstEnergy Corp.		1,279		37
Fiserv, Inc. (f)		1,388		143
FleetCor Technologies, Inc. (f)		203		48
Flex Ltd. (f)		1,600		18
FLIR Systems, Inc.		370		13
Flowserve Corp.		355		10
Fluor Corp.		378		3
FMC Corp.		264		28
Ford Motor Co.		69,775		465
Fortinet, Inc. (f)		415		49
Fortive Corp.		2,598		198
Fortune Brands Home & Security, Inc.		1,324		115
Fox Corp., Class A		1,128		31
Fox Corp., Class B (f)		504		14
Franklin Resources, Inc.		866		18
Freeport-McMoRan, Inc.		3,192		50
Gap, Inc. (The)		778		13
Garmin Ltd.		264		25
Gartner, Inc. (f)		217		27
General Dynamics Corp.		2,134		295
General Electric Co.		75,774		472
General Mills, Inc.		1,301		80
General Motors Co.		22,925		678
Genuine Parts Co.		508		48
Gilead Sciences, Inc.		2,884		182
Global Payments, Inc.		644		114
Globe Life, Inc.		274		22
GoDaddy, Inc., Class A (f)		507		39
Goldman Sachs Group, Inc. (The)		864		174
Goodyear Tire & Rubber Co. (The)		16,600		127
GrubHub, Inc. (f)		308		22
H&R Block, Inc.		722		12
Halliburton Co.		2,560		31
Hanesbrands, Inc.		1,149		18
Harley-Davidson, Inc.		452		11
Hartford Financial Services Group, Inc. (The)		963		35
Hasbro, Inc.		317		26
HCA Healthcare, Inc.		556		69
HD Supply Holdings, Inc. (f)		1,527		63

The accompanying notes are an integral part of the consolidated financial statements.
23

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

	Shares		Value (000)
United States (cont'd)
Healthpeak Properties, Inc. REIT		1,491	$	40
HEICO Corp.		494		52
HEICO Corp., Class A		698		62
Helmerich & Payne, Inc.		278		4
Henry Schein, Inc. (f)		520		31
Hershey Co. (The)		422		60
Hess Corp.		551		23
Hewlett Packard Enterprise Co.		3,956		37
Hilton Worldwide Holdings, Inc.		15,279		1,304
HollyFrontier Corp.		465		9
Hologic, Inc. (f)		543		36
Home Depot, Inc. (The)		2,632		731
Honeywell International, Inc.		6,193		1,019
Hormel Foods Corp.		643		31
Host Hotels & Resorts, Inc. REIT		2,194		24
Howmet Aerospace, Inc.		3,864		65
HP, Inc.		3,524		67
Humana, Inc.		264		109
Huntington Bancshares, Inc.		3,152		29
Huntington Ingalls Industries, Inc.		474		67
Hyatt Hotels Corp., Class A		6,219		332
IAC/InterActiveCorp (f)		174		21
IDEX Corp.		606		111
IDEXX Laboratories, Inc. (f)		205		81
IHS Markit Ltd.		3,231		254
Illinois Tool Works, Inc.		2,829		547
Illumina, Inc. (f)		517		160
Incyte Corp. (f)		550		49
Ingersoll Rand, Inc. (f)		2,854		102
Ingredion, Inc.		334		25
Intel Corp.		10,277		532
Intercontinental Exchange, Inc.		1,310		131
International Business Machines Corp.		2,121		258
International Flavors & Fragrances, Inc.		256		31
International Paper Co.		830		34
Interpublic Group of Cos., Inc. (The)		1,136		19
Intuit, Inc.		609		199
Intuitive Surgical, Inc. (f)		211		150
Invesco Ltd.		1,270		14
Invitation Homes, Inc. REIT		1,368		38
Ionis Pharmaceuticals, Inc. (f)		364		17
IPG Photonics Corp. (f)		229		39
IQVIA Holdings, Inc. (f)		498		78
Iron Mountain, Inc. REIT		797		21
Jack Henry & Associates, Inc.		170		28
Jacobs Engineering Group, Inc.		1,204		112
Jazz Pharmaceuticals PLC (f)		207		30
JB Hunt Transport Services, Inc.		759		96
Jefferies Financial Group, Inc.		788		14
JM Smucker Co. (The)		202		23
Johnson & Johnson		6,215		925
Johnson Controls International PLC		6,802		278

	Shares		Value (000)
Jones Lang LaSalle, Inc.		179	$	17
JPMorgan Chase & Co.		7,716		743
Juniper Networks, Inc.		1,112		24
Kansas City Southern		856		155
KB Home		10,455		401
Kellogg Co.		601		39
KeyCorp		2,947		35
Keysight Technologies, Inc. (f)		459		45
Kimberly-Clark Corp.		809		119
Kimco Realty Corp. REIT		1,385		16
Kinder Morgan, Inc.		4,644		57
KKR & Co., Inc., Class A		1,199		41
KLA Corp.		468		91
Knight-Swift Transportation Holdings, Inc.		1,142		46
Kohl's Corp.		471		9
Kraft Heinz Co. (The)		1,555		47
Kroger Co. (The)		1,880		64
L Brands, Inc.		701		22
L3Harris Technologies, Inc.		1,968		334
Laboratory Corp. of America Holdings (f)		247		47
Lam Research Corp.		426		141
Lamb Weston Holdings, Inc.		520		34
Las Vegas Sands Corp.		825		38
Lear Corp.		1,176		128
Leggett & Platt, Inc.		352		14
Leidos Holdings, Inc.		490		44
Lennar Corp., Class A		34,748		2,838
Lennox International, Inc.		435		119
Liberty Broadband Corp., Class C (f)		176		25
Liberty Global PLC, Class A (f)		543		11
Liberty Global PLC Series C (f)		1,349		28
Liberty Media Corp-Liberty SiriusXM, Class A (f)		305		10
Liberty Media Corp-Liberty SiriusXM, Class C (f)		490		16
Liberty Media Corp.-Liberty Formula One, Class C (f)		713		26
Lincoln National Corp.		717		22
Linde PLC		1,335		318
Live Nation Entertainment, Inc. (f)		521		28
LKQ Corp. (f)		988		27
Lockheed Martin Corp.		2,196		842
Loews Corp.		788		27
Louisiana-Pacific Corp.		3,078		91
Lowe's Cos., Inc.		1,866		309
Lululemon Athletica, Inc. (f)		185		61
LyondellBasell Industries N.V., Class A		632		45
M&T Bank Corp.		261		24
M/I Homes, Inc. (f)		3,281		151
Macerich Co. (The) REIT		313		2
Macy's, Inc.		848		5
ManpowerGroup, Inc.		307		23
Marathon Oil Corp.		2,355		10
Marathon Petroleum Corp.		1,560		46
Markel Corp. (f)		39		38

The accompanying notes are an integral part of the consolidated financial statements.
24

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

	Shares		Value (000)
United States (cont'd)
MarketAxess Holdings, Inc.		232	$	112
Marriott International, Inc., Class A		18,263		1,691
Marriott Vacations Worldwide Corp.		2,040		185
Marsh & McLennan Cos., Inc.		1,274		146
Martin Marietta Materials, Inc.		1,945		458
Marvell Technology Group Ltd.		1,389		55
Masco Corp.		9,738		537
Mastercard, Inc., Class A		2,238		757
Match Group, Inc. (f)		491		54
Maxim Integrated Products, Inc.		560		38
McCormick & Co., Inc.		232		45
McDonald's Corp.		1,716		377
McKesson Corp.		467		70
MDC Holdings, Inc.		6,968		328
Medtronic PLC		3,165		329
MercadoLibre, Inc. (f)		252		273
Merck & Co., Inc.		5,959		494
Meritage Homes Corp. (f)		4,219		466
MetLife, Inc.		1,860		69
Mettler-Toledo International, Inc. (f)		89		86
MGIC Investment Corp.		9,571		85
MGM Resorts International		1,497		33
Microchip Technology, Inc.		526		54
Micron Technology, Inc. (f)		2,597		122
Microsoft Corp.		16,844		3,543
Mid-America Apartment Communities, Inc. REIT		205		24
Middleby Corp. (The) (f)		195		17
Mohawk Industries, Inc. (f)		2,141		209
Molson Coors Brewing Co., Class B		567		19
Mondelez International, Inc., Class A		3,207		184
MongoDB, Inc. (f)		216		50
Monster Beverage Corp. (f)		1,039		83
Moody's Corp.		504		146
Mosaic Co. (The)		1,262		23
Motorola Solutions, Inc.		476		75
MSCI, Inc.		197		70
Mylan N.V. (f)		1,492		22
Nasdaq, Inc.		208		26
National Oilwell Varco, Inc.		1,144		10
National Retail Properties, Inc. REIT		471		16
Nektar Therapeutics (f)		510		8
NetApp, Inc.		767		34
Netflix, Inc. (f)		1,063		532
Newell Brands, Inc.		1,337		23
Newmont Corp.		1,884		120
News Corp., Class A		1,155		16
NextEra Energy, Inc.		1,206		335
Nielsen Holdings PLC		3,506		50
NIKE, Inc., Class B		2,936		369
NiSource, Inc.		1,126		25
Noble Energy, Inc.		1,470		13
Nordson Corp.		372		71

	Shares		Value (000)
Nordstrom, Inc.		302	$	4
Norfolk Southern Corp.		2,145		459
Northern Trust Corp.		532		41
Northrop Grumman Corp.		1,470		464
NortonLifeLock, Inc.		1,848		39
Norwegian Cruise Line Holdings Ltd. (f)		763		13
NRG Energy, Inc.		790		24
Nucor Corp.		856		38
NVIDIA Corp.		1,308	��	708
NVR, Inc. (f)		449		1,833
NXP Semiconductors N.V.		1,400		175
O'Reilly Automotive, Inc. (f)		171		79
Occidental Petroleum Corp.		2,563		26
OGE Energy Corp.		706		21
Okta, Inc. (f)		167		36
Old Dominion Freight Line, Inc.		981		177
Omnicom Group, Inc.		583		29
ON Semiconductor Corp. (f)		1,315		29
ONEOK, Inc.		1,349		35
Oracle Corp.		5,849		349
Otis Worldwide Corp.		3,858		241
Ovintiv, Inc.		909		7
Owens Corning		3,787		261
PACCAR, Inc.		2,991		255
Packaging Corp. of America		332		36
Palo Alto Networks, Inc. (f)		233		57
Parker Hannifin Corp.		1,043		211
Parsley Energy, Inc., Class A		795		7
Paychex, Inc.		840		67
Paycom Software, Inc. (f)		176		55
PayPal Holdings, Inc. (f)		2,565		505
Pentair PLC		1,495		68
People's United Financial, Inc.		1,279		13
PepsiCo, Inc.		3,280		455
PerkinElmer, Inc.		196		25
Perrigo Co., PLC		349		16
Pfizer, Inc.		13,122		482
Philip Morris International, Inc.		3,668		275
Phillips 66		1,097		57
Pinnacle West Capital Corp.		300		22
Pioneer Natural Resources Co.		496		43
Plains GP Holdings LP, Class A (f)		437		3
PNC Financial Services Group, Inc. (The)		1,051		116
Polaris, Inc.		199		19
PPG Industries, Inc.		521		64
PPL Corp.		1,665		45
Principal Financial Group, Inc.		773		31
Procter & Gamble Co. (The)		5,819		809
Progressive Corp. (The)		1,365		129
ProLogis, Inc. REIT		1,698		171
Prudential Financial, Inc.		1,033		66
PTC, Inc. (f)		299		25
Public Service Enterprise Group, Inc.		1,287		71

The accompanying notes are an integral part of the consolidated financial statements.
25

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

	Shares		Value (000)
United States (cont'd)
Public Storage REIT		454	$	101
Pulte Group, Inc.		30,126		1,395
PVH Corp.		262		16
Qorvo, Inc. (f)		230		30
QUALCOMM, Inc.		2,727		321
Quest Diagnostics, Inc.		275		31
Qurate Retail, Inc.		1,288		9
Ralph Lauren Corp.		282		19
Raymond James Financial, Inc.		345		25
Raytheon Technologies Corp.		12,999		748
Realty Income Corp. REIT		772		47
Regency Centers Corp. REIT		490		19
Regeneron Pharmaceuticals, Inc. (f)		185		104
Regions Financial Corp.		2,972		34
Reinsurance Group of America, Inc.		320		30
RenaissanceRe Holdings Ltd.		250		42
Republic Services, Inc.		1,904		178
ResMed, Inc.		409		70
Robert Half International, Inc.		1,072		57
Rockwell Automation, Inc.		974		215
Rollins, Inc.		1,482		80
Roper Technologies, Inc.		798		315
Ross Stores, Inc.		975		91
Royal Caribbean Cruises Ltd.		530		34
S&P Global, Inc.		577		208
Sabre Corp.		766		5
salesforce.com, Inc. (f)		1,907		479
SBA Communications Corp. REIT		198		63
Schlumberger Ltd.		3,173		49
Scotts Miracle-Gro Co. (The), Class A		1,559		238
Seagate Technology PLC		777		38
Sealed Air Corp.		448		17
Seattle Genetics, Inc. (f)		202		40
SEI Investments Co.		358		18
Sempra Energy		570		67
Sensata Technologies Holding PLC (f)		1,468		63
ServiceNow, Inc. (f)		546		265
Sherwin-Williams Co. (The)		191		133
Signature Bank		247		20
Simon Property Group, Inc. REIT		787		51
Sirius XM Holdings, Inc.		4,812		26
Skyline Champion Corp. (f)		1,565		42
Skyworks Solutions, Inc.		507		74
SL Green Realty Corp. REIT		295		14
Snap, Inc., Class A (f)		1,877		49
Snap-On, Inc.		554		82
Southern Co. (The)		2,484		135
Southwest Airlines Co.		1,338		50
Spectrum Brands Holdings, Inc.		14		1
Spirit AeroSystems Holdings, Inc., Class A		270		5
Splunk, Inc. (f)		427		80
Square, Inc., Class A (f)		818		133

	Shares		Value (000)
SS&C Technologies Holdings, Inc.		496	$	30
Stanley Black & Decker, Inc.		1,410		229
Starbucks Corp.		2,890		248
State Street Corp.		825		49
Steel Dynamics, Inc.		773		22
STERIS PLC		203		36
Stewart Information Services Corp.		636		28
Stryker Corp.		897		187
Sun Communities, Inc. REIT		206		29
SVB Financial Group (f)		239		58
Synchrony Financial		1,850		48
Synopsys, Inc. (f)		430		92
Sysco Corp.		1,109		69
T Rowe Price Group, Inc.		533		68
T-Mobile US, Inc. (f)		1,047		120
Take-Two Interactive Software, Inc. (f)		199		33
Tapestry, Inc.		793		12
Targa Resources Corp.		703		10
Target Corp.		1,194		188
TD Ameritrade Holding Corp.		793		31
TE Connectivity Ltd.		877		86
TechnipFMC PLC		1,303		8
Teledyne Technologies, Inc. (f)		216		67
Teleflex, Inc.		163		55
Tesla, Inc. (f)		1,145		491
Texas Instruments, Inc.		2,190		313
Textron, Inc.		2,130		77
Thermo Fisher Scientific, Inc.		1,039		459
Tiffany & Co.		184		21
TJX Cos., Inc. (The)		2,906		162
Toll Brothers, Inc.		13,700		667
Tractor Supply Co.		218		31
Trane Technologies PLC		2,090		253
TransDigm Group, Inc.		526		250
TransUnion		1,749		147
Travelers Cos., Inc. (The)		530		57
Trimble, Inc. (f)		579		28
TripAdvisor, Inc.		281		6
Truist Financial Corp.		3,002		114
Twilio, Inc., Class A (f)		200		49
Twitter, Inc. (f)		1,662		74
Tyson Foods, Inc., Class A		648		39
Uber Technologies, Inc. (f)		6,645		242
UDR, Inc. REIT		774		25
UFP Industries, Inc.		1,586		90
UGI Corp.		519		17
Ulta Beauty, Inc. (f)		197		44
Under Armour, Inc., Class A (f)		545		6
Under Armour, Inc., Class C (f)		559		5
Union Pacific Corp.		6,007		1,183
United Airlines Holdings, Inc. (f)		332		12
United Parcel Service, Inc., Class B		6,017		1,003
United Rentals, Inc. (f)		606		106

The accompanying notes are an integral part of the consolidated financial statements.
26

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

	Shares		Value (000)
United States (cont'd)
UnitedHealth Group, Inc.		2,225	$	694
Universal Health Services, Inc., Class B		192		21
Unum Group		748		13
US Bancorp		3,538		127
Vail Resorts, Inc.		241		52
Valero Energy Corp.		962		42
Varian Medical Systems, Inc. (f)		219		38
Veeva Systems, Inc., Class A (f)		245		69
Ventas, Inc. REIT		963		40
VEREIT, Inc. REIT		2,918		19
VeriSign, Inc. (f)		182		37
Verisk Analytics, Inc.		1,437		266
Verizon Communications, Inc.		9,531		567
Vertex Pharmaceuticals, Inc. (f)		606		165
VF Corp.		872		61
ViacomCBS, Inc., Class B		1,402		39
Visa, Inc., Class A		4,131		826
Vistra Energy Corp.		1,275		24
VMware, Inc., Class A (f)		194		28
Vornado Realty Trust REIT		505		17
Voya Financial, Inc.		512		25
Vulcan Materials Co.		4,075		552
Walgreens Boots Alliance, Inc.		1,920		69
Walmart, Inc.		3,203		448
Walt Disney Co. (The)		4,089		507
Waste Connections, Inc.		2,261		235
Waste Management, Inc.		3,831		434
Waters Corp. (f)		252		49
Watsco, Inc.		1,058		246
Wayfair, Inc., Class A (f)		214		62
WEC Energy Group, Inc.		820		79
Wells Fargo & Co.		10,017		235
Welltower, Inc. REIT		970		53
Western Digital Corp.		813		30
Western Union Co. (The)		1,332		29
Westinghouse Air Brake Technologies Corp.		1,622		100
Westlake Chemical Corp.		232		15
WestRock Co.		786		27
Weyerhaeuser Co. REIT		1,846		53
Whirlpool Corp.		219		40
Williams Cos., Inc. (The)		2,736		54
Willis Towers Watson PLC		257		54
Workday, Inc., Class A (f)		438		94
WP Carey, Inc. REIT		486		32
WR Berkley Corp.		519		32
WW Grainger, Inc.		407		145
Wyndham Hotels & Resorts, Inc.		4,039		204
Wynn Resorts Ltd.		338		24
Xcel Energy, Inc.		1,325		91
Xerox Holdings Corp.		721		14
Xilinx, Inc.		585		61
XPO Logistics, Inc. (f)		854		72

	Shares		Value (000)
Xylem, Inc.		1,696	$	143
Yum! Brands, Inc.		787		72
Zebra Technologies Corp., Class A (f)		186		47
Zillow Group, Inc., Class C (f)		339		34
Zimmer Biomet Holdings, Inc.		520		71
Zions Bancorp NA		502		15
Zoetis, Inc.		1,104		183
				107,783
Total Common Stocks (Cost $134,372)				172,528
Preferred Stock (0.0%)
United States (0.0%)
Qurate Retail, Inc. (f) (Cost $5)		41		4
	No. of Rights
Right (0.0%)
United States (0.0%)
Bristol-Myers Squibb Co. (f) (Cost $5)		2,295		5
	No. of Warrants
Warrants (0.0%)
France (0.0%)
CGG SA, expires 2/21/22 (f) (Cost $—)		59		—	@
United States (0.0%)
Occidental Petroleum Corp., expires 8/3/27 (f) (Cost $2)		357		1
Total Warrants (Cost $2)				1
	Shares
Short-Term Investments (13.1%)
Investment Company (11.7%)
Morgan Stanley Institutional Liquidity Funds — Government Portfolio — Institutional Class (See Note G) (Cost $44,327)		44,327,016		44,327
	Face Amount (000)
U.S. Treasury Security (1.4%)
U.S. Treasury Bill,
0.16%, 1/28/21 (j)(k) (Cost $5,153)	$	5,156		5,154
Total Short-Term Investments (Cost $49,480)				49,481
Total Investments (98.9%) (Cost $326,378) (l)(m)(n)				373,889
Other Assets in Excess of Liabilities (1.1%)				4,231
Net Assets (100.0%)			$	378,120

Country assignments and aggregations are based generally on third party vendor classifications and information, and may be different from the assignments and aggregations under the policies set forth in the Fund's prospectus and/or statement of additional information relating to geographic classifications.

(a)  Security is subject to delayed delivery.

(b)  144A security — Certain conditions for public sale may exist. Unless otherwise noted, these securities are deemed to be liquid.

The accompanying notes are an integral part of the consolidated financial statements.
27

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

(c)  Floating or variable rate securities: The rates disclosed are as of September 30, 2020. For securities based on a published reference rate and spread, the reference rate and spread are indicated in the description in the Consolidated Portfolio of Investments. Certain variable rate securities may not be based on a published reference rate and spread but are determined by the issuer or agent and are based on current market conditions. These securities do not indicate a reference rate and spread in their description in the Consolidated Portfolio of Investments.

(d)  Inverse Floating Rate Security — Interest rate fluctuates with an inverse relationship to an associated interest rate. Indicated rate is the effective rate at September 30, 2020.

(e)  Perpetual — One or more securities do not have a predetermined maturity date. Rates for these securities are fixed for a period of time, after which they revert to a floating rate. Interest rates in effect are as of September 30, 2020.

(f)  Non-income producing security.

(g)  Security trades on the Hong Kong exchange.

(h)  At September 30, 2020, the Fund held fair valued securities valued at $0, representing 0.0% of net assets. These securities have been fair valued as determined in good faith under procedures established by and under the general supervision of the Trust's (as defined herein) Trustees.

(i)  Consists of one or more classes of securities traded together as a unit; stocks with attached warrants.

(j)  All or a portion of the security was pledged to cover margin requirements for swap agreements.

(k)  Rate shown is the yield to maturity at September 30, 2020.

(l)  Securities are available for collateral in connection with securities purchased on a forward commitment basis, foreign currency forward exchange contracts, futures contracts and swap agreements.

(m)  The approximate fair value and percentage of net assets, $57,630,000 and 15.2%, respectively, represent the securities that have been fair valued under the fair valuation policy for international investments as described in Note A-1 within the Notes to the Consolidated Financial Statements.

(n)  At September 30, 2020, the aggregate cost for federal income tax purposes is approximately $336,492,000. The aggregate gross unrealized appreciation is approximately $54,120,000 and the aggregate gross unrealized depreciation is approximately $14,087,000, resulting in net unrealized appreciation of approximately $40,033,000.

@  Value is less than $500.

ADR  American Depositary Receipt.

CDI  CHESS Depositary Interest.

CVA  Certificaten Van Aandelen.

EURIBOR  Euro Interbank Offered Rate.

Euronext  Euronext Paris Exchange.

Euronext N.V.  Euronext Amsterdam Stock Market.

IO  Interest Only.

LIBOR  London Interbank Offered Rate.

LSE  London Stock Exchange.

MTN  Medium Term Note.

NYSE  New York Stock Exchange.

OAT  Obligations Assimilables du Trésor (French Treasury Obligation).

OFZ  Obilgatsyi Federal'novo Zaima (Russian Federal Loan Obligation).

OMXH  Helsinki Stock Exchange.

REIT  Real Estate Investment Trust.

REMIC  Real Estate Mortgage Investment Conduit.

SDR  Swedish Depositary Receipt.

SIX  Swiss Exchange.

SOFR  Secured Overnight Financing Rate.

SSE  Stockholm Stock Exchange.

TBA  To Be Announced.

Foreign Currency Forward Exchange Contracts:

The Fund had the following foreign currency forward exchange contracts open at September 30, 2020:

Counterparty	Contracts to Deliver (000)		In Exchange For (000)		Delivery Date	Unrealized Appreciation (Depreciation) (000)
Australia And New Zealand Banking Group	$	952	GBP	720	12/1/20	$	(23	)
Bank of America NA	$	154	CZK	3,385	12/1/20		(7	)
Bank of America NA	CNH	10,096	$	1,481	12/17/20		(—	@)
Bank of America NA	PLN	252	$	67	12/17/20		2
Bank of America NA	$	304	ILS	1,040	12/17/20		(—	@)
Bank of Montreal	HUF	11,918	$	39	12/17/20		1
Bank of New York Mellon	EUR	381	$	452	12/17/20		5
Barclays Bank PLC	EUR	320	$	383	12/1/20		8
Barclays Bank PLC	EUR	202	$	237	12/1/20		—	@
Barclays Bank PLC	NZD	1,513	$	989	12/1/20		(12	)
Barclays Bank PLC	$	6,655	JPY	708,528	12/1/20		68
Barclays Bank PLC	COP	2,621,457	$	705	12/17/20		23
Barclays Bank PLC	EUR	81	$	96	12/17/20		1
Barclays Bank PLC	$	1,654	CNY	11,353	12/17/20		5
BNP Paribas SA	JPY	43,263	$	410	12/1/20		(—	@)
BNP Paribas SA	$	156	COP	577,465	12/1/20		(6	)
BNP Paribas SA	$	155	PEN	545	12/1/20		(3	)
BNP Paribas SA	$	509	THB	15,946	12/1/20		(6	)
BNP Paribas SA	CAD	55	$	42	12/17/20		—	@

The accompanying notes are an integral part of the consolidated financial statements.
28

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

Foreign Currency Forward Exchange Contracts: (cont'd)

Counterparty	Contracts to Deliver (000)		In Exchange For (000)		Delivery Date	Unrealized Appreciation (Depreciation) (000)
BNP Paribas SA	CZK	3,331	$	145	12/17/20	$	—	@
BNP Paribas SA	EUR	241	$	283	12/17/20		—	@
BNP Paribas SA	HKD	685	$	88	12/17/20		(—	@)
BNP Paribas SA	INR	52,093	$	703	12/17/20		2
BNP Paribas SA	JPY	70,072	$	665	12/17/20		—	@
BNP Paribas SA	KRW	839,646	$	708	12/17/20		(10	)
BNP Paribas SA	NZD	172	$	115	12/17/20		2
BNP Paribas SA	RUB	48,037	$	636	12/17/20		23
BNP Paribas SA	RUB	14,337	$	183	12/17/20		—	@
BNP Paribas SA	SEK	234	$	27	12/17/20		1
BNP Paribas SA	TRY	41	$	5	12/17/20		—	@
BNP Paribas SA	TWD	1,768	$	61	12/17/20		—	@
BNP Paribas SA	$	206	EUR	177	12/17/20		1
BNP Paribas SA	$	1,170	GBP	910	12/17/20		5
BNP Paribas SA	$	163	HKD	1,261	12/17/20		(—	@)
BNP Paribas SA	$	19	IDR	285,595	12/17/20		—	@
BNP Paribas SA	$	11	PEN	39	12/17/20		(—	@)
Citibank NA	CNH	1,055	$	153	12/1/20		(2	)
Citibank NA	MXN	16,024	$	720	12/1/20		1
Citibank NA	$	7,331	EUR	6,152	12/1/20		(110	)
Citibank NA	$	353	SGD	482	12/1/20		—	@
Citibank NA	$	77	CZK	1,734	12/17/20		(2	)
Citibank NA	$	140	ILS	479	12/17/20		(—	@)
Citibank NA	$	7	THB	223	12/17/20		(—	@)
Commonwealth Bank of Australia	EUR	149	$	176	12/17/20		2
Commonwealth Bank of Australia	NZD	41	$	28	12/17/20		—	@
Credit Suisse International	EUR	103	$	122	12/17/20		1
Goldman Sachs International	MYR	960	$	230	12/1/20		(—	@)
Goldman Sachs International	RUB	13,367	$	178	12/1/20		7
Goldman Sachs International	$	92	HUF	27,675	12/1/20		(3	)
Goldman Sachs International	$	1,644	KRW	1,947,574	12/1/20		22
Goldman Sachs International	$	297	MXN	6,381	12/1/20		(11	)
Goldman Sachs International	$	154	RUB	11,405	12/1/20		(8	)
Goldman Sachs International	CLP	468,992	$	613	12/17/20		15
Goldman Sachs International	EUR	2,213	$	2,628	12/17/20		29
Goldman Sachs International	GBP	130	$	169	12/17/20		—	@
Goldman Sachs International	JPY	20,686	$	196	12/17/20		—	@
Goldman Sachs International	$	7,987	BRL	42,301	12/17/20		(471	)
Goldman Sachs International	$	226	CHF	205	12/17/20		(3	)
Goldman Sachs International	$	93	CZK	2,104	12/17/20		(2	)
JPMorgan Chase Bank NA	$	108	AUD	151	10/6/20		(—	@)
JPMorgan Chase Bank NA	AUD	151	$	109	12/1/20		—	@
JPMorgan Chase Bank NA	CAD	278	$	211	12/1/20		2
JPMorgan Chase Bank NA	$	827	CHF	746	12/1/20		(16	)
JPMorgan Chase Bank NA	$	600	CNH	4,085	12/1/20		—	@
JPMorgan Chase Bank NA	$	517	EUR	442	12/1/20		3
JPMorgan Chase Bank NA	$	227	GBP	169	12/1/20		(8	)
JPMorgan Chase Bank NA	$	13	GBP	10	12/1/20		—	@
JPMorgan Chase Bank NA	$	85	PLN	317	12/1/20		(3	)
JPMorgan Chase Bank NA	$	355	SEK	3,093	12/1/20		(9	)
JPMorgan Chase Bank NA	CAD	258	$	196	12/17/20		2
JPMorgan Chase Bank NA	EUR	2,261	$	2,684	12/17/20		29
JPMorgan Chase Bank NA	NOK	474	$	52	12/17/20		2
JPMorgan Chase Bank NA	$	190	GBP	147	12/17/20		1
JPMorgan Chase Bank NA	ZAR	10	$	1	12/17/20		—	@
JPMorgan Chase Bank NA	CNH	2,595	$	373	8/12/21		(2	)
JPMorgan Chase Bank NA	$	589	CNH	4,185	8/12/21		16
JPMorgan Chase Bank NA	$	10,322	CNH	73,272	8/12/21		268
State Street Bank and Trust Co.	AUD	100	$	73	12/17/20		1
UBS AG	GBP	378	$	487	10/5/20		—	@

The accompanying notes are an integral part of the consolidated financial statements.
29

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

Foreign Currency Forward Exchange Contracts: (cont'd)

Counterparty	Contracts to Deliver (000)		In Exchange For (000)		Delivery Date	Unrealized Appreciation (Depreciation) (000)
UBS AG	$	61	CAD	81	10/5/20	$	(—	@)
UBS AG	AUD	2,789	$	2,002	12/1/20		4
UBS AG	AUD	125	$	92	12/1/20		3
UBS AG	AUD	2,461	$	1,752	12/1/20		(12	)
UBS AG	CAD	81	$	61	12/1/20		—	@
UBS AG	DKK	379	$	60	12/1/20		1
UBS AG	EUR	230	$	273	12/1/20		2
UBS AG	$	3,966	CNH	27,457	12/1/20		67
UBS AG	$	487	GBP	378	12/1/20		(—	@)
UBS AG	$	26	JPY	2,746	12/1/20		(—	@)
UBS AG	$	52	NOK	454	12/1/20		(3	)
UBS AG	$	154	RON	625	12/2/20		(4	)
UBS AG	DKK	370	$	59	12/17/20		1
UBS AG	EUR	4,789	$	5,686	12/17/20		62
UBS AG	HKD	644	$	83	12/17/20		(—	@)
UBS AG	HUF	224,528	$	743	12/17/20		20
UBS AG	JPY	311,401	$	2,956	12/17/20		(—	@)
UBS AG	MXN	210,435	$	9,882	12/17/20		447
UBS AG	MXN	4,751	$	213	12/17/20		—	@
UBS AG	SGD	172	$	127	12/17/20		—	@
UBS AG	TRY	5,704	$	738	12/17/20		16
UBS AG	$	156	AUD	217	12/17/20		(—	@)
UBS AG	$	1,552	CHF	1,406	12/17/20		(23	)
UBS AG	$	231	MXN	5,242	12/17/20		5
UBS AG	ZAR	13,023	$	785	12/17/20		14
						$	431

Futures Contracts:

The Fund had the following futures contracts open at September 30, 2020:

	Number of Contracts		Expiration Date	Notional Amount (000)			Value (000)			Unrealized Appreciation (Depreciation) (000)
Long:
100 oz Gold Future (United States)		20	Dec-20	$	2		$	3,791		$	21
MSCI Emerging Market E Mini (United States)		81	Dec-20		4			4,409			1
NASDAQ 100 E Mini (United States)		9	Dec-20		—	@		2,053			54
NYMEX WTI Crude Oil Futures (United States)		46	Nov-21		46			1,984			5
S&P 500 E Mini Index (United States)		145	Dec-20		8			24,302			119
SGX MSCI Singapore (Singapore)		30	Oct-20	SGD	3			621			3
U.S. Treasury 2 yr. Note (United States)		16	Dec-20	$	3,200			3,535			2
U.S. Treasury Ultra Long Bond (United States)		79	Dec-20		7,900			12,634			10
Short:
Euro Stoxx 50 Index (Germany)		92	Dec-20	EUR	(1	)		(3,445	)		101
FTSE 100 Index (United Kingdom)		2	Dec-20	GBP	—	@		(151	)		5
German Euro BTP (Germany)		47	Dec-20	EUR	(4,700	)		(8,132	)		(103	)
NIKKEI 225 Index (Japan)		46	Dec-20	JPY	(23	)		(5,074	)		(50	)
U.S. Treasury 10 yr. Note (United States)		31	Dec-20	$	(3,100	)		(4,326	)		(—	@)
U.S. Treasury 10 yr. Ultra Long Bond (United States)		11	Dec-20		(1,100	)		(1,759	)		(4	)
U.S. Treasury 5 yr. Note (United States)		9	Dec-20		(900	)		(1,134	)		(2	)
U.S. Treasury Ultra Long Bond (United States)		39	Dec-20		(3,900	)		(8,651	)		71
										$	233

The accompanying notes are an integral part of the consolidated financial statements.
30

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

Interest Rate Swap Agreements:

The Fund had the following interest rate swap agreements open at September 30, 2020:

Swap Counterparty	Floating Rate Index	Pay/ Receive Floating Rate	Fixed Rate			Payment Frequency Paid/ Received	Maturity Date	Notional Amount (000)		Value (000)			Upfront Payment Paid (000)		Unrealized Appreciation (000)
JPMorgan Chase   Bank NA	3 Month KORIBOR	Pay		1.83	%	Quarterly/Quarterly	6/14/27	KRW	1,400,000	$	71		$	—	$	71
Morgan Stanley &  US CPI All Urban  Co. LLC*	Consumers Index	Receive		1.24		Semi-Annual/Quarterly	3/30/30	$	1,286		79			—		79
Morgan Stanley &  US CPI All Urban  Co. LLC*	Consumers Index	Receive		1.27		Semi-Annual/Quarterly	3/30/30		4,644		266			—		266
Morgan Stanley &  US CPI All Urban  Co. LLC*	Consumers Index	Receive		1.30		Semi-Annual/Quarterly	3/30/30		1,286		70			—		70
Morgan Stanley &  US CPI All Urban  Co. LLC*	Consumers Index	Receive		1.18		Semi-Annual/Quarterly	3/31/30		2,143		144			—		144
Morgan Stanley &  US CPI All Urban  Co. LLC*	Consumers Index	Receive		1.31		Semi-Annual/Quarterly	4/28/30		790		43			—		43
Morgan Stanley &  US CPI All Urban   Co. LLC*	Consumers Index	Receive		1.37		Semi-Annual/Quarterly	5/29/30		628		34			—		34
Morgan Stanley &  US CPI All Urban  Co. LLC*	Consumers Index	Receive		1.75		Semi-Annual/Quarterly	7/30/30		318		9			—		9
Morgan Stanley &  US CPI All Urban  Co. LLC*	Consumers Index	Receive		1.96		Semi-Annual/Quarterly	8/28/30		591		—	@		—		—	@
										$	716		$	—	$	716

Total Return Swap Agreements:

The Fund had the following total return swap agreements open at September 30, 2020:

Swap Counterparty	Index	Pay/Receive Total Return of Referenced Index	Floating Rate	Payment Frequency	Maturity Date	Notional Amount (000)		Value (000)			Upfront Payment Paid (000)		Unrealized Appreciation (Depreciation) (000)
Barclays Bank PLC	Barclays Custom Covid-19 Basket Index††	Pay	3 Month USD LIBOR plus 0.11%	Quarterly	9/9/21	$	978	$	(65	)	$	—	$	(65	)
BNP Paribas SA	MSCI Emerging Markets Index	Receive	3 Month USD LIBOR plus 0.28%	Quarterly	1/26/21		21,336		147			—		147
BNP Paribas SA	BNP Custom U.S. Banks Index††	Receive	3 Month USD LIBOR plus 0.15%	Quarterly	9/16/21		886		(56	)		—		(56	)
BNP Paribas SA	BNP Custom IPO Basket Index††	Pay	3 Month USD LIBOR plus 1.00%	Quarterly	9/24/21		252		(23	)		—		(23	)
BNP Paribas SA	BNP Custom IPO Basket Index††	Pay	3 Month USD LIBOR plus 1.00%	Quarterly	9/24/21		588		(65	)		—		(65	)
JPMorgan Chase Bank NA	MSCI Japan Net Total Return Index	Receive	3 Month USD LIBOR plus 0.15%	Quarterly	2/10/21		16,602		806			—		806
JPMorgan Chase Bank NA	JPM EMU Growth Index††	Pay	3 Month EUR EURIBOR plus 0.05%	Quarterly	5/14/21	EUR	2,519		95			—		95
JPMorgan Chase Bank NA	JPM EMU Low Vol Index††	Pay	3 Month EUR EURIBOR plus 0.05%	Quarterly	5/14/21		2,494		148			—		148
JPMorgan Chase Bank NA	JPM EMU Value Index††	Receive	3 Month EUR EURIBOR plus 0.14%	Quarterly	5/14/21		5,241		(524	)		—		(524	)

The accompanying notes are an integral part of the consolidated financial statements.
31

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

Total Return Swap Agreements: (cont'd)

Swap Counterparty	Index	Pay/Receive Total Return of Referenced Index	Floating Rate	Payment Frequency	Maturity Date	Notional Amount (000)		Value (000)			Upfront Payment Paid (000)		Unrealized Appreciation (Depreciation) (000)
JPMorgan Chase Bank NA	JPM U.S. SPX 1500 Low Vol Index††	Pay	3 Month USD LIBOR plus 0.10%	Quarterly	5/14/21	$	3,937	$	158		$	—	$	158
JPMorgan Chase Bank NA	JPM U.S. SPX 1500 Low Vol Index††	Pay	3 Month USD LIBOR plus 0.10%	Quarterly	5/14/21		3,912		157			—		157
JPMorgan Chase Bank NA	JPM U.S. SPX 1500 Low Vol Index††	Pay	3 Month USD LIBOR plus 0.10%	Quarterly	5/14/21		3,844		154			—		154
JPMorgan Chase Bank NA	JPM U.S. SPX 1500 Low Vol Index††	Pay	3 Month USD LIBOR plus 0.10%	Quarterly	5/14/21		313		(8	)		—		(8	)
JPMorgan Chase Bank NA	JPM U.S. SPX 1500 Value Index††	Receive	3 Month USD LIBOR plus 0.10%	Quarterly	5/14/21		4,172		(280	)		—		(280	)
JPMorgan Chase Bank NA	JPM U.S. SPX 1500 Value Index††	Receive	3 Month USD LIBOR plus 0.10%	Quarterly	5/14/21		4,075		(273	)		—		(273	)
JPMorgan Chase Bank NA	JPM U.S. SPX 1500 Value Index††	Receive	3 Month USD LIBOR plus 0.10%	Quarterly	5/14/21		3,828		(257	)		—		(257	)
JPMorgan Chase Bank NA	JPM U.S. SPX 1500 Value Index††	Receive	3 Month USD LIBOR plus 0.10%	Quarterly	5/14/21		427		16			—		16
JPMorgan Chase Bank NA	JPM U.S. SPX 500 Growth Index††	Pay	3 Month USD LIBOR plus 0.10%	Quarterly	5/14/21		9,097		83			—		83
JPMorgan Chase Bank NA	JPM U.S. SPX 500 Growth Index††	Pay	3 Month USD LIBOR plus 0.10%	Quarterly	5/14/21		69		(2	)		—		(2	)
JPMorgan Chase Bank NA	JPM U.S. SPX 500 Low Vol Index††	Pay	3 Month USD LIBOR plus 0.10%	Quarterly	5/14/21		8,382		16			—		16
JPMorgan Chase Bank NA	JPM U.S. SPX 500 Value Index††	Receive	3 Month USD LIBOR plus 0.10%	Quarterly	5/14/21		18,207		(902	)		—		(902	)
JPMorgan Chase Bank NA	JPM U.S. SPX 500 Value Index††	Receive	3 Month USD LIBOR plus 0.10%	Quarterly	5/14/21		89		3			—		3
JPMorgan Chase Bank NA	JPM IPO Index††	Pay	3 Month USD LIBOR plus 1.24%	Quarterly	9/1/21		1,237		162			—		162
								$	(510	)	$	—	$	(510	)

††  See tables below for details of the equity basket holdings underlying the swap.

The accompanying notes are an integral part of the consolidated financial statements.
32

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

The following table represents the equity basket holdings underlying the total return swap with Barclays Custom Covid-19 Basket Index as of September 30, 2020:

Security Description	Shares		Value (000)		Index Weight
Barclays Custom Covid-19 Basket Index
Atlassian Corp. PLC-Class A		25,005	$	4,546		8.98	%
Citrix Systems, Inc.		32,328		4,452		8.80
Crowdstrike Holdings, Inc. — A		35,167		4,829		9.54
Everbridge, Inc.		33,302		4,187		8.27
Netflix, Inc.		8,645		4,323		8.54
Okta, Inc.		21,771		4,656		9.20
Ringcentral Inc. — Class A		16,250		4,462		8.82
Roku, Inc.		27,234		5,142		10.17
Slack Technologies, Inc. — Class A		146,722		3,941		7.79
Zoom Video Communications — A		11,920		5,604		11.08
Zscaler, Inc.		31,686		4,458		8.81
Total			$	50,600		100.00	%

The following table represents the equity basket holdings underlying the total return swap with BNP Custom U.S. Banks Index as of September 30, 2020:

Security Description	Shares		Value (000)		Index Weight
BNP Custom U.S. Banks Index
Bank of America Corp.		308,343	$	7,428		21.41	%
CIT Group, Inc.		3,298		58		0.17
Citigroup, Inc.		79,236		3,416		9.85
Citizens Financial Group		15,687		397		1.14
Comerica, Inc.		5,287		202		0.58
East West Bancorp, Inc.		4,961		162		0.47
Fifth Third Bancorp		25,079		535		1.54
First Republic Bank		5,750		627		1.81
Huntington Bancshares, Inc.		35,695		327		0.94
JPMorgan Chase & Co.		110,953		10,681		30.80
Keycorp		34,389		410		1.18
M & T Bank Corp.		4,440		409		1.18
People'S United Financial		13,619		140		0.40
PNC Financial Services Group		15,425		1,695		4.89
Regions Financial Corp.		34,597		399		1.15
Signature Bank		1,907		158		0.46
SVB Financial Group		1,793		431		1.24
Truist Financial Corp.		45,852		1,745		5.03
US Bancorp		51,605		1,850		5.33
Wells Fargo & Co.		146,120		3,435		9.90
Zions Bancorp NA		6,245		182		0.53
Total			$	34,687		100.00	%

The following table represents the equity basket holdings underlying the total return swap with BNP Custom IPO Basket Index as of September 30, 2020:

Security Description	Shares		Value (000)		Index Weight
BNP Custom IPO Basket Index
Berkeley Lights, Inc.		1,878	$	143		13.15	%
Duck Creek Technologies, Inc.		5,023		228		20.93
Li Auto Inc — ADR		21,351		371		34.04
Oak Street Health, Inc.		4,323		231		21.18
Vertex, Inc. — Class A		5,073		117		10.70
Total			$	1,090		100.00	%

The accompanying notes are an integral part of the consolidated financial statements.
33

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

The following table represents the equity basket holdings underlying the total return swap with JPM EMU Growth Index as of September 30, 2020:

Security Description	Shares		Value (000)		Index Weight
JPM EMU Growth Index
Adyen N.V.		121	$	224		2.27	%
Air Liquide SA		1,245		198		2.01
Airbus SE		2,785		203		2.06
Amundi SA		2,767		195		1.98
Beiersdorf AG		1,726		196		1.99
Biomerieux		1,272		200		2.03
Cellnex Telecom SA		3,347		204		2.07
Davide Campari-Milano N.V.		20,698		226		2.30
Delivery Hero SE		1,747		201		2.04
Deutsche Bank Ag-Registered		22,658		191		1.94
Deutsche Boerse AG		1,119		197		2.00
Deutsche Wohnen SE		4,237		212		2.16
E.On SE		17,599		194		1.98
Elia Group SA		1,968		196		2.00
Ferrari N.V.		1,129		207		2.11
Ferrovial SA		8,424		205		2.08
Finecobank SPA		13,970		192		1.96
Galapagos N.V.		1,082		154		1.56
Gea Group AG		5,579		196		2.00
Getlink SE		13,590		185		1.88
Groupe Bruxelles Lambert SA		2,306		208		2.11
Hannover Rueck SE		1,206		187		1.90
Hermes International		257		222		2.25
Iberdrola SA		16,004		197		2.00
Iliad SA		1,046		193		1.96
Just Eat Takeaway		1,866		209		2.13
Knorr-Bremse AG		1,755		207		2.10
Koninklijke Dsm N.V.		1,341		221		2.24
L'Oreal		638		208		2.11
Muenchener Rueckver AG		758		192		1.96
Nemetschek SE		2,752		202		2.05
Pernod Ricard SA		1,183		189		1.92
Prosus N.V.		2,108		194		1.98
Sartorius AG-Vorzug		539		221		2.25
Sartorius Stedim Biotech		661		228		2.31
Scout24 AG		2,398		209		2.13
Siemens Gamesa Renewable Energy		8,649		234		2.38
Symrise AG		1,640		227		2.31
Teamviewer AG		3,758		186		1.89
Teleperformance		695		215		2.18
Terna SPA		28,262		198		2.01
Ubisoft Entertainment		2,467		223		2.26
Umicore		4,434		185		1.88
Vonovia SE		3,146		216		2.20
Vopak		3,826		216		2.19
Wendel		2,153		195		1.99
Wolters Kluwer		2,588		221		2.25
Zalando SE		2,771		260		2.64
Total			$	9,839		100.00	%

The accompanying notes are an integral part of the consolidated financial statements.
34

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

The following table represents the equity basket holdings underlying the total return swap with JPM EMU Low Vol Index as of September 30, 2020:

Security Description	Shares		Value (000)		Index Weight
JPM EMU Low Vol Index
Ageas		5,626	$	230		2.36	%
Air Liquide SA		1,299		206		2.12
Akzo Nobel N.V.		2,291		232		2.39
Allianz SE-REG		1,022		196		2.01
Alstom		3,842		191		1.97
Asml Holding N.V.		597		220		2.26
Assicurazioni Generali		14,543		205		2.11
Dassault Systemes SA		1,186		222		2.28
Deutsche Boerse AG		1,168		205		2.11
Eni SPA		24,582		193		1.98
Essilorluxottica		1,676		228		2.34
Ferrovial SA		8,790		214		2.20
Getlink SE		14,181		193		1.98
Groupe Bruxelles Lambert SA		2,406		217		2.23
Hannover Rueck SE		1,258		195		2.00
Heineken Holding N.V.		2,540		198		2.03
Henkel AG & Co. KGaA		2,508		235		2.41
Hermes International		268		231		2.38
Iberdrola SA		16,700		206		2.11
ICADE		3,331		187		1.92
Koninklijke Dsm N.V.		1,399		231		2.37
Koninklijke Kpn N.V.		84,259		198		2.04
Legrand SA		2,780		222		2.28
L'Oreal		666		217		2.23
Lvmh Moet Hennessy Louis Vui		497		233		2.39
Mapfre SA		116,773		183		1.88
Merck KGaA		1,649		241		2.47
Michelin		2,047		220		2.26
Muenchener Rueckver AG-REG		791		201		2.06
Pernod Ricard SA		1,234		197		2.02
Prosus N.V.		2,200		203		2.08
Proximus		10,718		196		2.01
Recordati Industria Chimica		4,043		207		2.13
Red Electrica Corporacion SA		11,279		212		2.17
Sanofi		2,052		205		2.11
SAP SE		1,347		210		2.15
Schneider Electric SE		1,822		226		2.33
Snam SPA		41,110		211		2.17
Symrise AG		1,711		237		2.43
Teleperformance		725		224		2.30
Terna SPA		29,491		206		2.12
Total SE		5,716		196		2.01
UCB SA		1,712		195		2.00
Vinci SA		2,447		205		2.11
Vonovia SE		3,283		225		2.32
Wolters Kluwer		2,701		231		2.37
Total			$	9,736		100.00	%

The accompanying notes are an integral part of the consolidated financial statements.
35

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

The following table represents the equity basket holdings underlying the total return swap with JPM EMU Value Index as of September 30, 2020:

Security Description	Shares		Value (000)		Index Weight
JPM EMU Value Index
ACS Actividades Cons Y Serv		8,932	$	203		2.08	%
Aercap Holdings N.V.		7,450		188		1.93
Atlantia SPA		12,945		204		2.10
Atos SE		2,448		197		2.03
Banco Bilbao Vizcaya Argenta		65,842		183		1.88
Banco Santander SA		96,583		181		1.86
Bayer AG-REG		3,067		192		1.97
Bayerische Motoren Werke AG		3,191		232		2.38
Bayerische Motoren Werke-Pref		2,022		111		1.14
BNP Paribas		5,058		184		1.89
Bouygues SA		5,727		199		2.04
Capgemini SE		1,635		210		2.16
Carrefour SA		13,335		214		2.20
Casino Guichard Perrachon		7,639		186		1.91
CNP Assurances		17,147		215		2.21
Compagnie De Saint Gobain		5,492		232		2.39
Credit Agricole SA		21,423		188		1.93
Deutsche Telekom AG-REG		6,206		104		1.07
EIFFAGE		2,368		194		1.99
ENGIE		15,072		202		2.07
Fresenius Medical Care AG		2,352		199		2.04
Fresenius SE & Co. KGaA		4,188		191		1.96
Heidelbergcement AG		3,716		228		2.35
Hochtief AG		2,581		201		2.07
Ipsen		2,090		219		2.26
Klepierre		13,140		185		1.90
Koninklijke Ahold Delhaize N		7,273		215		2.21
Lanxess AG		4,001		230		2.37
Leonardo SPA		32,386		190		1.95
Metro AG		22,526		225		2.31
Natixis		86,353		195		2.00
Naturgy Energy Group SA		11,352		228		2.34
Nokia Oyj		41,949		165		1.69
Omv AG		6,546		180		1.85
Orange		8,968		93		0.96
Peugeot SA		12,871		234		2.40
Pirelli & C SPA		51,777		222		2.29
Publicis Groupe		6,331		205		2.10
Raiffeisen Bank International		12,234		187		1.93
Repsol SA		26,793		180		1.85
Societe Generale SA		13,903		184		1.90
Solvay SA		2,689		232		2.38
Stora Enso Oyj-R SHS		16,447		258		2.65
Suez		16,050		297		3.06
Telefonica SA		49,821		172		1.76
Unibail-Rodamco-Westfield		4,298		159		1.63
Uniper SE		5,963		193		1.98
Volkswagen AG		1,292		226		2.32
Volkswagen AG-Pref		1,367		220		2.26
Total			$	9,732		100.00	%

The accompanying notes are an integral part of the consolidated financial statements.
36

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

The following table represents the equity basket holdings underlying the total return swap with JPM U.S. SPX 1500 Low Vol Index as of September 30, 2020:

Security Description	Shares		Value (000)		Index Weight
JPM U.S. SPX 1500 Low Vol Index
Abbott Laboratories		520	$	57		0.57	%
Agilent Technologies, Inc.		528		53		0.54
Air Products & Chemicals, Inc.		188		56		0.56
Akamai Technologies, Inc.		463		51		0.52
Alexandria Real Estate Equity		297		48		0.48
Allstate Corp.		544		51		0.52
American Express Co.		560		56		0.56
American Tower Corp.		204		49		0.50
Amerisafe, Inc.		825		47		0.48
Amerisourcebergen Corp.		501		49		0.49
Amgen, Inc.		212		54		0.54
Amphenol Corp. — Cl A		487		53		0.53
Analog Devices, Inc.		449		52		0.53
Aptargroup, Inc.		441		50		0.50
Arthur J Gallagher & Co.		493		52		0.52
At&T, Inc.		1,767		50		0.51
Atmos Energy Corp.		497		48		0.48
Autozone, Inc.		43		51		0.51
Badger Meter, Inc.		817		53		0.54
Baxter International, Inc.		630		51		0.51
Booking Holdings, Inc.		32		54		0.55
Brady Corp. — Cl A		1,118		45		0.45
Broadcom, Inc.		163		59		0.61
Brookline BanCorp, Inc.		5,476		47		0.48
Brown & Brown, Inc.		1,150		52		0.52
Cable One, Inc.		28		53		0.53
Cabot Oil & Gas Corp.		2,738		48		0.48
Carrier Global Corp.		1,895		58		0.58
CDW Corp.		446		53		0.54
Cerner Corp.		761		55		0.55
Chemed Corp.		104		50		0.50
Chevron Corp.		617		44		0.45
Cisco Systems, Inc.		1,110		44		0.44
City Holding Co.		837		48		0.49
Cme Group, Inc.		321		54		0.54
Cms Energy Corp.		831		51		0.51
Columbia Sportswear Co.		710		62		0.62
Comcast Corp. — Class A		1,221		56		0.57
Commerce Bancshares, Inc.		910		51		0.52
Community Bank System, Inc.		937		51		0.51
Conocophillips		1,426		47		0.47
Corning, Inc.		1,694		55		0.55
Costco Wholesale Corp.		159		56		0.57
Cousins Properties, Inc.		1,728		49		0.50
Crown Castle Intl Corp.		319		53		0.53
Cvb Financial Corp.		2,902		48		0.49
Daktronics, Inc.		3,894		15		0.16
Danaher Corp.		253		55		0.55
Deckers Outdoor Corp.		253		56		0.56
Digital Realty Trust, Inc.		326		48		0.48
Dollar General Corp.		271		57		0.57
Dominion Energy, Inc.		652		51		0.52
Domino'S Pizza, Inc.		135		58		0.58

The accompanying notes are an integral part of the consolidated financial statements.
37

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

Security Description	Shares		Value (000)		Index Weight
Dorman Products, Inc.		639	$	58		0.58	%
Douglas Emmett, Inc.		1,818		46		0.46
Dril-Quip, Inc.		1,529		38		0.38
Dsp Group, Inc.		3,410		45		0.45
Duke Energy Corp.		625		55		0.56
Duke Realty Corp.		1,320		49		0.49
Dunkin' Brands Group, Inc.		772		63		0.64
Easterly Government Properties		2,177		49		0.49
Eaton Corp. PLC		552		56		0.57
Ecolab, Inc.		284		57		0.57
Emcor Group, Inc.		736		50		0.50
Encore Wire Corp.		1,043		48		0.49
Estee Lauder Companies — Cl A		264		58		0.58
Ethan Allen Interiors, Inc.		4,270		58		0.58
Eversource Energy		585		49		0.49
Expeditors Intl Wash, Inc.		610		55		0.56
Exponent, Inc.		628		45		0.46
Extra Space Storage, Inc.		514		55		0.55
Exxon Mobil Corp.		1,239		43		0.43
Factset Research Systems, Inc.		150		50		0.51
Fidelity National Info Serv		352		52		0.52
Firstcash, Inc.		927		53		0.53
Fiserv, Inc.		521		54		0.54
Flowers Foods, Inc.		2,252		55		0.55
Fulton Financial Corp.		5,419		51		0.51
Garmin Ltd.		524		50		0.50
Gatx Corp.		861		55		0.55
General Dynamics Corp.		354		49		0.49
Gentex Corp.		1,943		50		0.50
Gilead Sciences, Inc.		730		46		0.46
Graco, Inc.		979		60		0.60
Hasbro, Inc.		699		58		0.58
Hawaiian Electric Industries		1,453		48		0.49
Heartland Express, Inc.		2,589		48		0.48
Helen Of Troy Ltd.		267		52		0.52
Henry Schein, Inc.		738		43		0.44
Heritage Financial Corp.		2,803		52		0.52
Hershey Co. (The)		361		52		0.52
Hill-Rom Holdings, Inc.		547		46		0.46
Hilton Worldwide Holdings In		700		60		0.60
Home Depot, Inc.		197		55		0.55
Hp, Inc.		2,946		56		0.56
Idex Corp.		315		57		0.58
Ihs Markit Ltd.		642		50		0.51
Illinois Tool Works		282		54		0.55
Intercontinental Exchange In		544		54		0.55
Intuit, Inc.		168		55		0.55
Jack Henry & Associates, Inc.		288		47		0.47
Jacobs Engineering Group, Inc.		578		54		0.54
Johnson & Johnson		355		53		0.53
Kilroy Realty Corp.		918		48		0.48
Kinder Morgan, Inc.		3,731		46		0.46
Kkr Real Estate Finance Trust		3,146		52		0.52
Lennox International, Inc.		194		53		0.53
Life Storage, Inc.		533		56		0.56
Lincoln Electric Holdings		569		52		0.53

The accompanying notes are an integral part of the consolidated financial statements.
38

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

Security Description	Shares		Value (000)		Index Weight
Linde PLC		214	$	51		0.51	%
Lindsay Corp.		532		51		0.52
Lockheed Martin Corp.		139		53		0.54
Lowe'S Cos, Inc.		348		58		0.58
Marsh & Mclennan Cos		452		52		0.52
Maximus, Inc.		693		47		0.48
Mcdonald'S Corp.		269		59		0.59
Merck & Co., Inc.		634		53		0.53
Microsoft Corp.		242		51		0.51
Microstrategy, Inc.-Cl A		423		64		0.64
Mid-America Apartment Comm		448		52		0.52
Mondelez International, Inc. — A		943		54		0.55
Monro, Inc.		896		36		0.37
Msa Safety, Inc.		433		58		0.58
Msc Industrial Direct Co.-A		774		49		0.49
N B T BanCorp., Inc.		1,767		47		0.48
Nasdaq, Inc.		402		49		0.50
National Instruments Corp.		1,430		51		0.51
National Oilwell Varco, Inc.		4,517		41		0.41
National Storage Affiliates		1,691		55		0.56
Neenah, Inc.		1,145		43		0.43
Netscout Systems, Inc.		2,031		44		0.45
Newmarket Corp.		142		48		0.49
Newmont Corp.		768		49		0.49
Nike, Inc. — Cl B		532		67		0.67
Northern Trust Corp.		660		51		0.52
Northrop Grumman Corp.		162		51		0.51
Northwest Bancshares, Inc.		5,331		49		0.49
Nucor Corp.		1,221		55		0.55
Nvr, Inc.		14		55		0.56
Old National BanCorp.		3,774		47		0.48
Old Republic Intl Corp.		3,200		47		0.47
Omnicom Group		975		48		0.49
O'Reilly Automotive, Inc.		110		51		0.51
Otis Worldwide Corp.		828		52		0.52
Pepsico, Inc.		383		53		0.53
Power Integrations, Inc.		863		48		0.48
Ppg Industries, Inc.		488		60		0.60
Procter & Gamble Co. (The)		399		55		0.56
Ps Business Parks, Inc.		376		46		0.46
Public Storage		267		60		0.60
Reliance Steel & Aluminum		518		53		0.53
Republic Services, Inc.		599		56		0.56
Resmed, Inc.		259		44		0.45
Rex American Resources Corp.		581		38		0.38
Ross Stores, Inc.		596		56		0.56
S & T BanCorp., Inc.		2,522		45		0.45
S&P Global, Inc.		149		54		0.54
Safety Insurance Group, Inc.		698		48		0.49
Schlumberger Ltd.		2,797		44		0.44
Seacor Holdings, Inc.		1,696		49		0.50
Service Corp. International		1,176		50		0.50
Sherwin-Williams Co. (The)		82		57		0.57
Sonoco Products Co.		1,002		51		0.51
Southside Bancshares, Inc.		1,911		47		0.47
Southwest Airlines Co.		1,658		62		0.63

The accompanying notes are an integral part of the consolidated financial statements.
39

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

Security Description	Shares		Value (000)		Index Weight
Standard Motor Prods		1,132	$	51		0.51	%
Starbucks Corp.		693		60		0.60
Steris PLC		325		57		0.58
Stryker Corp.		273		57		0.57
Texas Instruments, Inc.		405		58		0.58
Thermo Fisher Scientific, Inc.		125		55		0.56
Tjx Companies, Inc.		1,009		56		0.56
Tompkins Financial Corp.		819		47		0.47
Tootsie Roll Inds		1,658		51		0.52
Toro Co.		726		61		0.61
Tractor Supply Company		355		51		0.51
Trane Technologies PLC		467		57		0.57
Tyler Technologies, Inc.		144		50		0.50
UDR, Inc.		1,491		49		0.49
Union Pacific Corp.		304		60		0.60
Unitedhealth Group, Inc.		172		54		0.54
Verisign, Inc.		247		51		0.51
Vertex Pharmaceuticals, Inc.		187		51		0.51
Visa, Inc. — Class A Shares		275		55		0.55
Walmart, Inc.		405		57		0.57
Washington Federal, Inc.		2,274		47		0.48
Waste Management, Inc.		480		54		0.55
Watts Water Technologies — A		609		61		0.61
Westamerica BanCorporation		875		48		0.48
Williams Cos, Inc.		2,655		52		0.52
Yum! Brands, Inc.		576		53		0.53
Zoetis, Inc.		339		56		0.56
Total			$	9,940		100.00	%

The following table represents the equity basket holdings underlying the total return swap with JPM U.S. SPX 1500 Value Index as of September 30, 2020:

Security Description	Shares		Value (000)		Index Weight
JPM U.S. SPX 1500 Value Index
AAR Corp.		3,015	$	57		0.55	%
Advansix, Inc.		4,275		55		0.54
Alliance Data Systems Corp.		1,151		48		0.47
American Equity Invt Life Hl		1,986		44		0.43
American International Group		1,610		44		0.43
Apogee Enterprises, Inc.		2,348		50		0.49
Arcbest Corp.		1,653		51		0.50
Archer-Daniels-Midland Co.		1,205		56		0.55
Archrock, Inc.		7,476		40		0.39
Asbury Automotive Group		513		50		0.49
Associated BancCorp.		3,989		50		0.49
Atlas Air Worldwide Holdings		970		59		0.58
Autonation, Inc.		978		52		0.51
Avanos Medical, Inc.		1,661		55		0.54
Avis Budget Group, Inc.		2,038		54		0.52
Avnet, Inc.		1,915		49		0.48
Azz, Inc.		1,617		55		0.54
Baker Hughes Co.		3,310		44		0.43
Bank Of New York Mellon Corp.		1,436		49		0.48
Big Lots, Inc.		1,263		56		0.55
Biogen, Inc.		186		53		0.52
Bonanza Creek Energy, Inc.		2,847		54		0.52

The accompanying notes are an integral part of the consolidated financial statements.
40

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

Security Description	Shares		Value (000)		Index Weight
Boston Private Finl Holding		8,828	$	49		0.48	%
Brinker International, Inc.		1,991		85		0.83
Brixmor Property Group, Inc.		4,538		53		0.52
Cadence BanCorp.		6,641		57		0.56
Callon Petroleum Co.		4,384		21		0.21
Capri Holdings Ltd.		3,693		66		0.65
Cardinal Health, Inc.		891		42		0.41
Cardtronics PLC — A		2,353		47		0.46
Carnival Corp.		3,958		60		0.59
Cato Corp.-Class A		6,011		47		0.46
Centerpoint Energy, Inc.		2,678		52		0.51
Central Garden And Pet Co. — A		1,421		51		0.50
Century Communities, Inc.		1,417		60		0.59
Centurylink, Inc.		5,279		53		0.52
Citigroup, Inc.		1,027		44		0.43
Citizens Financial Group		2,135		54		0.53
Cno Financial Group, Inc.		3,381		54		0.53
Cnx Resources Corp.		5,097		48		0.47
Comerica, Inc.		1,360		52		0.51
Commercial Metals Co.		2,428		49		0.47
Computer Programs & Systems		1,440		40		0.39
Comtech Telecommunications		3,128		44		0.43
Cooper-Standard Holding		4,538		60		0.59
Corecivic, Inc.		5,800		46		0.45
Crane Co.		899		45		0.44
Customers BanCorp., Inc.		4,433		50		0.49
Cvs Health Corp.		810		47		0.46
Dana, Inc.		4,297		53		0.52
Dave & Buster'S Entertainment		4,297		65		0.64
Deluxe Corp.		1,761		45		0.44
Diamondrock Hospitality Co.		11,420		58		0.57
Dine Brands Global, Inc.		1,165		64		0.62
Diodes, Inc.		985		56		0.54
Discovery, Inc. — C		2,704		53		0.52
Donnelley Financial Solution		5,347		71		0.70
Dorian Lpg Ltd.		5,780		46		0.45
Dxc Technology Co.		2,850		51		0.50
Dxp Enterprises, Inc.		2,832		46		0.45
Eastman Chemical Co.		688		54		0.53
Ebay, Inc.		915		48		0.47
Ebix, Inc.		2,295		47		0.46
Edgewell Personal Care Co.		1,677		47		0.46
Endo International PLC		14,291		47		0.46
Enova International, Inc.		3,199		52		0.51
Enpro Industries, Inc.		1,075		61		0.59
Exelon Corp.		1,362		49		0.48
Fifth Third BanCorp.		2,634		56		0.55
First Solar, Inc.		850		56		0.55
Fnb Corp.		7,000		47		0.46
Fresh Del Monte Produce, Inc.		2,237		51		0.50
Garrett Motion, Inc.		9,238		32		0.31
Genworth Financial, Inc. — Cl A		25,236		85		0.83
Geo Group, Inc. (The)		4,703		53		0.52
G-Iii Apparel Group Ltd.		5,372		70		0.69
Gms, Inc.		2,099		51		0.49
Graham Holdings Co. — Class B		129		52		0.51

The accompanying notes are an integral part of the consolidated financial statements.
41

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

Security Description	Shares		Value (000)		Index Weight
Granite Point Mortgage Trust		7,642	$	54		0.53	%
Greenbrier Companies, Inc.		2,042		60		0.59
Greif, Inc. — Cl A		1,450		53		0.51
Group 1 Automotive, Inc.		584		52		0.50
Hibbett Sports, Inc.		2,221		87		0.85
Hologic, Inc.		725		48		0.47
Hope BanCorp., Inc.		6,196		47		0.46
Howmet Aerospace, Inc.		3,419		57		0.56
Insight Enterprises, Inc.		1,018		58		0.56
Integer Holdings Corp.		789		47		0.46
Interface, Inc.		6,379		39		0.38
Intl Business Machines Corp.		416		51		0.49
Istar, Inc.		4,491		53		0.52
J2 Global, Inc.		884		61		0.60
Janus Henderson Group PLC		2,471		54		0.52
KB Home		1,523		58		0.57
KBR, Inc.		2,260		51		0.49
Kelly Services, Inc. — A		3,440		59		0.57
Koppers Holdings, Inc.		2,042		43		0.42
Kraton Corp.		3,790		68		0.66
Lannett Co, Inc.		8,264		50		0.49
Lantheus Holdings, Inc.		3,890		49		0.48
Laredo Petroleum, Inc.		3,558		35		0.34
Lincoln National Corp.		1,377		43		0.42
Lyondellbasell Indu — Cl A		833		59		0.57
M/I Homes, Inc.		1,219		56		0.55
Macerich Co. (The)		6,807		46		0.45
Manpowergroup, Inc.		750		55		0.54
Marcus Corporation		3,887		30		0.29
Mastec, Inc.		1,211		51		0.50
Matrix Service Co.		4,129		34		0.34
Mdu Resources Group, Inc.		2,443		55		0.54
Meredith Corp.		3,583		47		0.46
Meritor, Inc.		2,229		47		0.46
Meta Financial Group, Inc.		2,793		54		0.52
Metlife, Inc.		1,387		52		0.50
Micron Technology, Inc.		1,027		48		0.47
Minerals Technologies, Inc.		1,010		52		0.50
Mohawk Industries, Inc.		651		64		0.62
Molson Coors Beverage Co. — B		1,405		47		0.46
Moog, Inc. — Class A		959		61		0.60
Mts Systems Corp.		2,737		52		0.51
Mylan N.V.		3,162		47		0.46
Natus Medical, Inc.		2,944		50		0.49
Navient Corp.		6,379		54		0.53
Netgear, Inc.		1,607		50		0.48
Nrg Energy, Inc.		1,546		48		0.46
Odp Corp. (The)		2,431		47		0.46
Oge Energy Corp.		1,599		48		0.47
Orthofix Medical, Inc.		1,659		52		0.50
Oshkosh Corp.		648		48		0.47
Owens & Minor, Inc.		3,041		76		0.75
Pebblebrook Hotel Trust		4,989		63		0.61
Penn Virginia Corp.		5,184		51		0.50
Photronics, Inc.		4,251		42		0.41
Pilgrim'S Pride Corp.		3,422		51		0.50

The accompanying notes are an integral part of the consolidated financial statements.
42

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

Security Description	Shares		Value (000)		Index Weight
Polaris, Inc.		488	$	46		0.45	%
Powell Industries, Inc.		1,145		28		0.27
Pra Health Sciences, Inc.		479		49		0.47
Progress Software Corp.		1,439		53		0.52
Propetro Holding Corp.		9,355		38		0.37
Quanex Building Products		2,895		53		0.52
Quanta Services, Inc.		1,256		66		0.65
Quinstreet, Inc.		4,347		69		0.67
Reinsurance Group Of America		608		58		0.57
Renewable Energy Group, Inc.		1,820		97		0.95
Resideo Technologies, Inc.		4,656		51		0.50
RPT Realty		8,551		47		0.45
RR Donnelley & Sons Co.		32,657		48		0.47
Ruth'S Hospitality Group, Inc.		7,827		87		0.85
Sabra Health Care Reit, Inc.		3,595		50		0.48
Sally Beauty Holdings, Inc.		4,479		39		0.38
Sanmina Corp.		1,735		47		0.46
Scansource, Inc.		2,171		43		0.42
Schweitzer-Mauduit Intl, Inc.		1,574		48		0.47
Select Medical Holdings Corp.		2,727		57		0.55
Service Properties Trust		8,077		64		0.63
Signet Jewelers Ltd.		4,690		88		0.86
Simmons First Natl Corp. — Cl A		3,089		49		0.48
Simon Property Group, Inc.		848		55		0.54
Skywest, Inc.		1,914		57		0.56
Sl Green Realty Corp.		1,127		52		0.51
Smart Global Holdings, Inc.		1,831		50		0.49
Spartannash Co.		2,412		39		0.39
Standex International Corp.		950		56		0.55
Sterling BanCorp.		4,623		49		0.48
Stifel Financial Corp.		1,056		53		0.52
Summit Hotel Properties, Inc.		10,224		53		0.52
Suncoke Energy, Inc.		15,443		53		0.52
Sykes Enterprises, Inc.		1,809		62		0.60
Syneos Health, Inc.		795		42		0.41
Synnex Corp.		408		57		0.56
Synovus Financial Corp.		2,585		55		0.53
Tanger Factory Outlet Center		8,264		50		0.49
Tapestry, Inc.		3,878		61		0.59
Timken Co.		1,038		56		0.55
Tyson Foods, Inc. — Cl A		829		49		0.48
Ugi Corp.		1,560		51		0.50
Ultra Clean Holdings, Inc.		1,714		37		0.36
United Therapeutics Corp.		444		45		0.44
Universal Health Services-B		480		51		0.50
Unum Group		3,031		51		0.50
Vanda Pharmaceuticals, Inc.		4,894		47		0.46
Varex Imaging Corp.		3,237		41		0.40
Viacomcbs, Inc. — Class B		2,013		56		0.55
Viad Corp.		3,522		73		0.72
Wabash National Corp.		4,452		53		0.52
Waddell & Reed Financial — A		3,580		53		0.52
Walgreens Boots Alliance, Inc.		1,259		45		0.44
Walker & Dunlop, Inc.		1,016		54		0.53
Warrior Met Coal, Inc.		3,201		55		0.53
Weingarten Realty Investors		3,036		51		0.50

The accompanying notes are an integral part of the consolidated financial statements.
43

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

Security Description	Shares		Value (000)		Index Weight
Westrock Co.		1,860	$	65		0.63	%
Whitestone REIT		8,021		48		0.47
Wyndham Destinations, Inc.		1,968		61		0.59
Xerox Holdings Corp.		3,231		61		0.59
Xperi Holding Corp.		2,726		31		0.31
Total			$	10,234		100.00	%

The following table represents the equity basket holdings underlying the total return swap with JPM U.S. SPX 500 Growth Index as of September 30, 2020:

Security Description	Shares		Value (000)		Index Weight
JPM U.S. SPX 500 Growth Index
Abiomed, Inc.		318	$	88		0.87	%
Adobe, Inc.		219		107		1.06
Advanced Micro Devices		1,262		103		1.02
Air Products & Chemicals, Inc.		352		105		1.04
Alexandria Real Estate Equity		556		89		0.88
Align Technology, Inc.		341		112		1.10
Amazon.Com, Inc.		32		99		0.98
American Tower Corp.		382		92		0.91
American Water Works Co., Inc.		667		97		0.95
Ansys, Inc.		311		102		1.01
Aon PLC — Class A		490		101		1.00
Apache Corp.		6,237		59		0.58
Arthur J Gallagher & Co.		924		98		0.96
Autodesk, Inc.		409		95		0.93
Ball Corp.		1,322		110		1.09
Berkshire Hathaway, Inc. — Cl B		492		105		1.03
Blackrock, Inc.		169		95		0.94
Boeing Co. (The)		604		100		0.99
Brown-Forman Corp. — Class B		1,420		107		1.06
Cadence Design System, Inc.		877		94		0.92
Chipotle Mexican Grill, Inc.		85		106		1.05
Church & Dwight Co., Inc.		1,050		98		0.97
Cintas Corp.		328		109		1.08
Clorox Company		423		89		0.88
Cme Group, Inc.		601		101		0.99
Cms Energy Corp.		1,557		96		0.94
Copart, Inc.		1,051		111		1.09
Costco Wholesale Corp.		298		106		1.04
Crown Castle Intl Corp.		597		99		0.98
Dexcom, Inc.		221		91		0.90
Domino'S Pizza, Inc.		253		108		1.06
Ecolab, Inc.		532		106		1.05
Edwards Lifesciences Corp.		1,257		100		0.99
Equifax, Inc.		602		94		0.93
Equinix, Inc.		126		96		0.94
Estee Lauder Companies — Cl A		495		108		1.07
Eversource Energy		1,096		92		0.90
Fastenal Co.		2,066		93		0.92
First Republic Bank		868		95		0.94
Fortinet, Inc.		709		84		0.83
Gap, Inc. (The)		7,478		127		1.26
Hess Corp.		1,967		81		0.80
Hilton Worldwide Holdings In		1,312		112		1.11
Idex Corp.		590		108		1.06

The accompanying notes are an integral part of the consolidated financial statements.
44

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

Security Description	Shares		Value (000)		Index Weight
Idexx Laboratories, Inc.		250	$	98		0.97	%
Ihs Markit Ltd.		1,202		94		0.93
Illinois Tool Works		527		102		1.01
Illumina, Inc.		246		76		0.75
Incyte Corp.		963		86		0.85
Intercontinental Exchange In		1,018		102		1.01
Intl Flavors & Fragrances		787		96		0.95
Intuit, Inc.		315		103		1.01
Intuitive Surgical, Inc.		142		101		1.00
Jack Henry & Associates, Inc.		539		88		0.87
Linde PLC		401		96		0.94
Live Nation Entertainment In		2,101		113		1.12
Marathon Petroleum Corp.		2,542		75		0.74
Marketaxess Holdings, Inc.		192		92		0.91
Marsh & Mclennan Cos		846		97		0.96
Mastercard, Inc. — A		314		106		1.05
Mccormick & Co.-Non Vtg Shares		499		97		0.96
Mcdonald'S Corp.		504		111		1.09
Mettler-Toledo International		106		102		1.01
Monster Beverage Corp.		1,259		101		1.00
Moody'S Corp.		349		101		1.00
Msci, Inc.		264		94		0.93
Nasdaq, Inc.		752		92		0.91
National Oilwell Varco, Inc.		8,459		77		0.76
Netflix, Inc.		197		98		0.97
Nextera Energy, Inc.		353		98		0.97
Nike, Inc. — Cl B		997		125		1.24
Nvidia Corp.		223		120		1.19
Old Dominion Freight Line		537		97		0.96
Otis Worldwide Corp.		1,551		97		0.96
Paycom Software, Inc.		340		106		1.05
Paypal Holdings, Inc.		497		98		0.97
Prologis, Inc.		934		94		0.93
Resmed, Inc.		485		83		0.82
Rockwell Automation, Inc.		444		98		0.97
Rollins, Inc.		1,852		100		0.99
Roper Technologies, Inc.		225		89		0.88
S&P Global, Inc.		280		101		1.00
Salesforce.Com, Inc.		483		121		1.19
Sba Communications Corp.		321		102		1.01
Schlumberger Ltd.		5,237		81		0.80
Servicenow, Inc.		223		108		1.07
Sherwin-Williams Co. (The)		153		107		1.05
Starbucks Corp.		1,299		112		1.10
TJX Companies, Inc.		1,889		105		1.04
T-Mobile US, Inc.		917		105		1.04
Transdigm Group, Inc.		225		107		1.06
Tyler Technologies, Inc.		269		94		0.93
Under Armour, Inc. — Class A		10,138		114		1.11
Under Armour, Inc. — Class C		11,153		110		1.08
Verisign, Inc.		462		95		0.94
Verisk Analytics, Inc.		524		97		0.96
Wec Energy Group, Inc.		1,047		101		1.00
West Pharmaceutical Services		352		97		0.96
Wynn Resorts Ltd.		1,342		96		0.95
Xcel Energy, Inc.		1,426		98		0.97

The accompanying notes are an integral part of the consolidated financial statements.
45

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

Security Description	Shares		Value (000)		Index Weight
Yum! Brands, Inc.		1,078	$	98		0.97	%
Zoetis, Inc.		635		105		1.04
Total			$	10,125		100.00	%

The following table represents the equity basket holdings underlying the total return swap with JPM U.S. SPX 500 Low Vol Index as of September 30, 2020:

Security Description	Shares		Value (000)		Index Weight
JPM U.S. SPX 500 Low Vol Index
3M Co.		693	$	111		1.08	%
Abbott Laboratories		1,035		113		1.10
Accenture PLC — Cl A		459		104		1.01
Air Products & Chemicals, Inc.		374		111		1.09
Akamai Technologies, Inc.		922		102		0.99
Alexandria Real Estate Equity		591		95		0.92
Alphabet, Inc. — Cl A		70		103		1.00
Alphabet, Inc. — Cl C		71		104		1.01
Ameren Corporation		1,314		104		1.01
American Tower Corp.		406		98		0.96
Amgen, Inc.		421		107		1.04
Aon PLC — Class A		520		107		1.05
Arthur J Gallagher & Co.		982		104		1.01
Atmos Energy Corp.		989		95		0.92
Automatic Data Processing		775		108		1.05
Autozone, Inc.		86		102		0.99
Ball Corp.		1,404		117		1.14
Baxter International, Inc.		1,253		101		0.98
Berkshire Hathaway, Inc. — Cl B		523		111		1.09
Booking Holdings, Inc.		63		108		1.05
C.H. Robinson Worldwide, Inc.		1,114		114		1.11
Cabot Oil & Gas Corp.		5,448		95		0.92
Carrier Global Corp.		3,771		115		1.12
Cerner Corp.		1,514		109		1.07
Chevron Corp.		1,228		88		0.86
Cme Group, Inc.		639		107		1.04
Cms Energy Corp.		1,654		102		0.99
Coca-Cola Co. (The)		2,250		111		1.08
Colgate-Palmolive Co.		1,360		105		1.02
Comcast Corp — Class A		2,429		112		1.10
Costco Wholesale Corp.		316		112		1.09
Crown Castle Intl Corp.		635		106		1.03
Danaher Corp.		504		108		1.06
Dollar General Corp.		540		113		1.10
Dominion Energy, Inc.		1,297		102		1.00
Duke Realty Corp.		2,626		97		0.94
Ecolab, Inc.		565		113		1.10
Eli Lilly & Co.		682		101		0.98
Eversource Energy		1,164		97		0.95
Expeditors Intl Wash, Inc.		1,214		110		1.07
Exxon Mobil Corp.		2,465		85		0.83
Fidelity National Info Serv		699		103		1.00
Fiserv, Inc.		1,036		107		1.04
Garmin Ltd.		1,042		99		0.96
Hershey Co. (The)		719		103		1.00
Hilton Worldwide Holdings In		1,394		119		1.16

The accompanying notes are an integral part of the consolidated financial statements.
46

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

Security Description	Shares		Value (000)		Index Weight
Home Depot, Inc.		391	$	109		1.06	%
Honeywell Internationa,l Inc.		701		115		1.13
Idex Corp.		626		114		1.11
Ihs Markit Ltd.		1,277		100		0.98
Illinois Tool Works		560		108		1.06
Intercontinental Exchange In		1,082		108		1.06
Intuit, Inc.		334		109		1.06
Jack Henry & Associates, Inc.		572		93		0.91
Johnson & Johnson		707		105		1.03
Kimberly-Clark Corp.		687		101		0.99
Linde PLC		426		102		0.99
Marsh & Mclennan Cos		899		103		1.01
Mastercard, Inc. — A		333		113		1.10
Mcdonald'S Corp.		536		118		1.16
Medtronic PLC		1,070		111		1.08
Merck & Co. Inc.		1,262		105		1.02
Microsoft Corp.		481		101		0.99
Nasdaq, Inc.		799		98		0.96
Nike, Inc. — Cl B		1,059		133		1.30
Northrop Grumman Corp.		322		102		0.99
Oracle Corp.		1,861		111		1.08
Otis Worldwide Corp.		1,648		103		1.00
Packaging Corp Of America		1,086		118		1.15
Paychex, Inc.		1,432		114		1.11
Pepsico, Inc.		762		106		1.03
Procter & Gamble Co. (The)		793		110		1.08
Progressive Corp.		1,159		110		1.07
Public Storage		532		118		1.15
Republic Services, Inc.		1,191		111		1.08
Roper Technologies, Inc.		239		95		0.92
Ross Stores, Inc.		1,185		111		1.08
S&P Global, Inc.		297		107		1.04
Starbucks Corp.		1,380		119		1.17
Steris PLC		647		114		1.11
Thermo Fisher Scientific, Inc.		249		110		1.07
Tjx Companies, Inc.		2,007		112		1.09
T-Mobile US, Inc.		975		111		1.09
Travelers Cos, Inc. (The)		911		99		0.96
UDR, Inc.		2,966		97		0.94
Union Pacific Corp.		605		119		1.17
Verisign, Inc.		491		101		0.98
Verisk Analytics, Inc.		557		103		1.01
Visa, Inc. — Class A Shares		546		109		1.07
Vulcan Materials Co.		886		120		1.17
Walt Disney Co. (The)		895		111		1.08
Waste Management, Inc.		956		108		1.05
Wec Energy Group, Inc.		1,112		108		1.05
Williams Cos Inc		5,282		104		1.01
Wr Berkley Corp.		1,676		103		1.00
Zoetis, Inc.		674		111		1.09
Total			$	10,259		100.00	%

The accompanying notes are an integral part of the consolidated financial statements.
47

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

The following table represents the equity basket holdings underlying the total return swap with JPM U.S. SPX 500 Value Index as of September 30, 2020:

Security Description	Shares		Value (000)		Index Weight
JPM U.S. SPX 500 Value Index
AES Corp.		6,681	$	121		1.20	%
Aflac, Inc.		1,428		52		0.51
Alexion Pharmaceuticals, Inc.		963		110		1.09
Allstate Corp.		525		49		0.49
American International Group		3,143		87		0.86
Amerisourcebergen Corp.		967		94		0.93
Anthem, Inc.		373		100		0.99
Archer-Daniels-Midland Co.		2,353		109		1.08
Baker Hughes Co.		6,463		86		0.85
Biogen, Inc.		363		103		1.02
Borgwarner, Inc.		2,735		106		1.05
Cardinal Health, Inc.		1,740		82		0.81
Cbre Group, Inc, — A		2,443		115		1.14
Centene Corp.		1,601		93		0.93
Centerpoint Energy, Inc.		5,228		101		1.00
Centurylink, Inc.		10,307		104		1.03
Cf Industries Holdings, Inc.		3,212		99		0.98
Cigna Corp.		584		99		0.98
Cisco Systems, Inc.		2,142		84		0.84
Citigroup, Inc.		2,005		86		0.86
Citizens Financial Group		4,169		105		1.05
Cognizant Tech Solutions — A		1,485		103		1.02
Comerica, Inc.		2,655		102		1.01
Cvs Health Corp.		1,582		92		0.92
Delta Air Lines, Inc.		4,008		123		1.22
Devon Energy Corp.		9,529		90		0.89
Discovery, Inc. — A		4,733		103		1.02
Discovery, Inc. — C		5,280		103		1.03
Dxc Technology Co.		5,565		99		0.99
Eastman Chemical Co.		1,344		105		1.04
Edison International		1,873		95		0.94
Exelon Corp.		2,659		95		0.94
Fedex Corp.		597		150		1.49
Fifth Third Bancorp		5,143		110		1.09
General Dynamics Corp.		684		95		0.94
General Motors Co.		3,940		117		1.16
Hartford Financial Services Group		2,405		89		0.88
Hewlett Packard Enterprise		10,213		96		0.95
Host Hotels & Resorts, Inc.		9,797		106		1.05
Howmet Aerospace, Inc.		6,676		112		1.11
HP, Inc.		5,684		108		1.07
Huntington Ingalls Industries		576		81		0.80
Intel Corp.		2,091		108		1.07
International Paper Co.		2,850		116		1.15
Interpublic Group Of Cos, Inc.		2,742		46		0.45
Intl Business Machines Corp.		813		99		0.98
Jm Smucker Co. (The)		910		105		1.04
Johnson Controls Internation		2,595		106		1.05
Juniper Networks, Inc.		3,992		86		0.85
Kimco Realty Corp.		9,108		103		1.02
Kinder Morgan, Inc.		3,600		44		0.44
Kohls Corp.		5,226		97		0.96
Kraft Heinz Co. (The)		2,903		87		0.86

The accompanying notes are an integral part of the consolidated financial statements.
48

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

Security Description	Shares		Value (000)		Index Weight
Kroger Co.		2,878	$	98		0.97	%
Leidos Holdings, Inc.		1,028		92		0.91
Lennar Corp. — A		1,372		112		1.11
Lincoln National Corp.		2,688		84		0.84
LKQ Corp.		3,524		98		0.97
Lyondellbasell Indu — Cl A		1,626		115		1.14
Metlife, Inc.		2,708		101		1.00
Micron Technology, Inc.		2,005		94		0.93
Mohawk Industries, Inc.		1,271		124		1.23
Molson Coors Beverage Co. — B		2,744		92		0.91
Mylan N.V.		6,174		92		0.91
Netapp, Inc.		2,362		104		1.03
Newell Brands, Inc.		6,163		106		1.05
Nielsen Holdings PLC		7,005		99		0.99
Nrg Energy, Inc.		3,018		93		0.92
Nucor Corp.		2,357		106		1.05
Omnicom Group		941		47		0.46
Oneok, Inc.		3,592		93		0.93
Perrigo Co. PLC		1,845		85		0.84
Pfizer, Inc.		2,634		97		0.96
Phillips 66		1,653		86		0.85
Ppl Corp.		3,809		104		1.03
Principal Financial Group		2,351		95		0.94
Pultegroup, Inc.		2,294		106		1.05
Quanta Services Inc		2,452		130		1.29
Raytheon Technologies Corp.		1,756		101		1.00
Robert Half Intl, Inc.		1,981		105		1.04
Seagate Technology		2,257		111		1.10
Simon Property Group, Inc.		1,655		107		1.06
Sl Green Realty Corp.		2,200		102		1.01
Snap-On, Inc.		703		103		1.03
Synchrony Financial		4,446		116		1.15
Tapestry, Inc.		7,572		118		1.17
Te Connectivity Ltd.		1,125		110		1.09
Textron, Inc.		2,814		102		1.01
Tyson Foods, Inc. — Cl A		1,618		96		0.95
United Airlines Holdings, Inc.		3,169		110		1.09
United Rentals, Inc.		633		110		1.10
Universal Health Services-B		937		100		1.00
Unum Group		5,917		100		0.99
Viacomcbs, Inc. — Class B		3,930		110		1.09
Vornado Realty Trust		2,969		100		0.99
Wabtec Corp.		1,643		102		1.01
Walgreens Boots Alliance, Inc.		2,459		88		0.88
Western Digital Corp.		2,301		84		0.83
Western Union Co.		2,086		45		0.44
Westrock Co.		3,631		126		1.25
Whirlpool Corp.		614		113		1.12
Xerox Holdings Corp.		6,309		118		1.17
Total			$	10,086		100.00	%

The accompanying notes are an integral part of the consolidated financial statements.
49

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Portfolio of Investments (cont'd)

Global Strategist Portfolio

The following table represents the equity basket holdings underlying the total return swap with JPM IPO Index as of September 30, 2020:

Security Description	Shares		Value (000)		Index Weight
JPM IPO Index
Kingsoft Cloud Holdings — ADR		64,698	$	1,911		22.49	%
Lemonade, Inc.		37,954		1,887		22.22
Ncino, Inc.		15,421		1,229		14.47
Shift4 Payments, Inc. — Class A		34,820		1,684		19.83
Vroom, Inc.		34,421		1,782		20.99
Total			$	8,493		100.00	%

@    Value is less than $500.

*    Cleared swap agreement, the broker is Morgan Stanley & Co. LLC.

BTP    Buoni del Tesoro Poliennali.

CPI    Consumer Price Index.

EURIBOR    Euro Interbank Offered Rate.

KORIBOR    Korea Interbank Offered Rate.

LIBOR    London Interbank Offered Rate.

NYMEX    New York Mercantile Exchange.

SGX    Singapore Exchange Ltd.

WTI    West Texas Intermediate.

AUD  —  Australian Dollar

BRL  —  Brazilian Real

CAD  —  Canadian Dollar

CHF  —  Swiss Franc

CLP  —  Chilean Peso

CNH  —  Chinese Yuan Renminbi Offshore

CNY  —  Chinese Yuan Renminbi

COP  —  Colombian Peso

CZK  —  Czech Koruna

DKK  —  Danish Krone

EUR  —  Euro

GBP  —  British Pound

HKD  —  Hong Kong Dollar

HUF  —  Hungarian Forint

IDR  —  Indonesian Rupiah

ILS  —  Israeli Shekel

INR  —  Indian Rupee

JPY  —  Japanese Yen

KRW  —  South Korean Won

MXN  —  Mexican Peso

MYR  —  Malaysian Ringgit

NOK  —  Norwegian Krone

NZD  —  New Zealand Dollar

PEN  —  Peruvian Nuevo Sol

PLN  —  Polish Zloty

RON  —  Romanian New Leu

RUB  —  Russian Ruble

SEK  —  Swedish Krona

SGD  —  Singapore Dollar

THB  —  Thai Baht

TRY  —  Turkish Lira

TWD  —  Taiwan Dollar

USD  —  United States Dollar

ZAR  —  South African Rand

Portfolio Composition

Classification	Percentage of Total Investments
Common Stocks		46.2	%
Fixed Income Securities		40.6
Short-Term Investments		13.2
Other**		0.0	***
Total Investments		100.0	%****

**  Industries and/or investment types representing less than 5% of total investments.

***  Amount is less than 0.05%.

****  Does not include open long/short futures contracts with a value of approximately $97,195,000 and net unrealized appreciation of approximately $243,000. Does not include open foreign currency forward exchange contracts with net unrealized appreciation of approximately $431,000. Also does not include open swap agreements with net unrealized appreciation of approximately $206,000.

The accompanying notes are an integral part of the consolidated financial statements.
50

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Global Strategist Portfolio

Consolidated Statement of Assets and Liabilities	September 30, 2020 (000)
Assets:
Investments in Securities of Unaffiliated Issuers, at Value (Cost $282,051)	$	329,562
Investment in Security of Affiliated Issuer, at Value (Cost $44,327)		44,327
Total Investments in Securities, at Value (Cost $326,378)		373,889
Foreign Currency, at Value (Cost $1,035)		1,035
Receivable for Investments Sold		9,770
Receivable for Variation Margin on Futures Contracts		3,334
Unrealized Appreciation on Swap Agreements		2,016
Due from Broker		1,224
Unrealized Appreciation on Foreign Currency Forward Exchange Contracts		1,190
Interest Receivable		1,120
Dividends Receivable		178
Tax Reclaim Receivable		172
Receivable for Variation Margin on Swap Agreements		10
Receivable for Fund Shares Sold		7
Receivable from Affiliate		1
Other Assets		63
Total Assets		394,009
Liabilities:
Payable for Investments Purchased		10,306
Unrealized Depreciation on Swap Agreements		2,455
Bank Overdraft		1,223
Unrealized Depreciation on Foreign Currency Forward Exchange Contracts		759
Payable for Advisory Fees		374
Due to Broker		312
Payable for Trustees' Fees and Expenses		110
Payable for Professional Fees		82
Payable for Custodian Fees		58
Payable for Shareholder Services Fees — Class A		35
Payable for Distribution and Shareholder Services Fees — Class L		8
Payable for Distribution and Shareholder Services Fees — Class C		1
Payable for Sub Transfer Agency Fees — Class I		6
Payable for Sub Transfer Agency Fees — Class A		24
Payable for Sub Transfer Agency Fees — Class L		2
Payable for Sub Transfer Agency Fees — Class C		—	@
Payable for Administration Fees		25
Payable for Fund Shares Redeemed		19
Payable for Transfer Agency Fees — Class I		2
Payable for Transfer Agency Fees — Class A		6
Payable for Transfer Agency Fees — Class L		1
Payable for Transfer Agency Fees — Class C		1
Payable for Transfer Agency Fees — Class IS		1
Deferred Capital Gain Country Tax		5
Other Liabilities		74
Total Liabilities		15,889
Net Assets	$	378,120
Net Assets Consist of:
Paid-in-Capital	$	335,034
Total Distributable Earnings		43,086
Net Assets	$	378,120

The accompanying notes are an integral part of the consolidated financial statements.
51

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Global Strategist Portfolio

Consolidated Statement of Assets and Liabilities (cont'd)	September 30, 2020 (000)
CLASS I:
Net Assets	$	34,031
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		2,115,836
Net Asset Value, Offering and Redemption Price Per Share	$	16.08
CLASS A:
Net Assets	$	170,643
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		10,727,972
Net Asset Value, Redemption Price Per Share	$	15.91
Maximum Sales Load		5.25	%
Maximum Sales Charge	$	0.88
Maximum Offering Price Per Share	$	16.79
CLASS L:
Net Assets	$	12,773
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		815,306
Net Asset Value, Offering and Redemption Price Per Share	$	15.67
CLASS C:
Net Assets	$	1,435
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		92,659
Net Asset Value, Offering and Redemption Price Per Share	$	15.49
CLASS IS:
Net Assets	$	159,238
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		9,891,840
Net Asset Value, Offering and Redemption Price Per Share	$	16.10

@  Amount is less than $500.

The accompanying notes are an integral part of the consolidated financial statements.
52

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Global Strategist Portfolio

Consolidated Statement of Operations	Year Ended September 30, 2020 (000)
Investment Income:
Dividends from Securities of Unaffiliated Issuers (Net of $167 of Foreign Taxes Withheld)	$	3,510
Interest from Securities of Unaffiliated Issuers (Net of $9 of Foreign Taxes Withheld)		3,419
Dividends from Security of Affiliated Issuer (Note G)		417
Total Investment Income		7,346
Expenses:
Advisory Fees (Note B)		1,750
Shareholder Services Fees — Class A (Note D)		431
Distribution and Shareholder Services Fees — Class L (Note D)		95
Distribution and Shareholder Services Fees — Class C (Note D)		15
Administration Fees (Note C)		311
Custodian Fees (Note F)		269
Professional Fees		241
Sub Transfer Agency Fees — Class I		38
Sub Transfer Agency Fees — Class A		118
Sub Transfer Agency Fees — Class L		8
Sub Transfer Agency Fees — Class C		1
Pricing Fees		134
Registration Fees		96
Shareholder Reporting Fees		56
Transfer Agency Fees — Class I (Note E)		9
Transfer Agency Fees — Class A (Note E)		25
Transfer Agency Fees — Class L (Note E)		5
Transfer Agency Fees — Class C (Note E)		3
Transfer Agency Fees — Class IS (Note E)		2
Trustees' Fees and Expenses		12
Other Expenses		39
Total Expenses		3,658
Waiver of Advisory Fees (Note B)		(144	)
Rebate from Morgan Stanley Affiliate (Note G)		(94	)
Reimbursement of Class Specific Expenses — Class I (Note B)		(32	)
Reimbursement of Class Specific Expenses — Class C (Note B)		(2	)
Reimbursement of Class Specific Expenses — Class IS (Note B)		(2	)
Net Expenses		3,384
Net Investment Income		3,962
Realized Gain (Loss):
Investments Sold (Net of $4 of Capital Gain Country Tax)		4,500
Foreign Currency Forward Exchange Contracts		(2,253	)
Foreign Currency Translation		(35	)
Futures Contracts		147
Swap Agreements		(3,424	)
Net Realized Loss		(1,065	)
Change in Unrealized Appreciation (Depreciation):
Investments (Net of Increase in Deferred Capital Gain Country Tax of $1)		13,984
Foreign Currency Forward Exchange Contracts		1,463
Foreign Currency Translation		42
Futures Contracts		708
Swap Agreements		1,382
Net Change in Unrealized Appreciation (Depreciation)		17,579
Net Realized Loss and Change in Unrealized Appreciation (Depreciation)		16,514
Net Increase in Net Assets Resulting from Operations	$	20,476

The accompanying notes are an integral part of the consolidated financial statements.
53

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Global Strategist Portfolio

Consolidated Statements of Changes in Net Assets	Year Ended September 30, 2020 (000)			Year Ended September 30, 2019 (000)
Increase (Decrease) in Net Assets:
Operations:
Net Investment Income	$	3,962		$	5,153
Net Realized Gain (Loss)		(1,065	)		1,003
Net Change in Unrealized Appreciation (Depreciation)		17,579			4,495
Net Increase in Net Assets Resulting from Operations		20,476			10,651
Dividends and Distributions to Shareholders:
Class I		(1,022	)		(7,553	)
Class A		(2,927	)		(25,417	)
Class L		(214	)		(1,941	)
Class C		(28	)		(218	)
Class IS		(2,790	)		(20	)
Total Dividends and Distributions to Shareholders		(6,981	)		(35,149	)
Capital Share Transactions:(1)
Class I:
Subscribed		5,888			6,077
Distributions Reinvested		1,019			7,518
Redeemed		(31,374	)		(13,423	)
Class A:
Subscribed		2,167			9,231
Distributions Reinvested		2,875			24,946
Redeemed		(37,743	)		(39,012	)
Class L:
Exchanged		321			404
Distributions Reinvested		209			1,901
Redeemed		(1,507	)		(4,829	)
Class C:
Subscribed		208			654
Distributions Reinvested		28			217
Redeemed		(709	)		(670	)
Class IS:
Subscribed		83			148,417
Distributions Reinvested		2,790			19
Redeemed		(937	)		(66	)
Net Increase (Decrease) in Net Assets Resulting from Capital Share Transactions		(56,682	)		141,384
Total Increase (Decrease) in Net Assets		(43,187	)		116,886
Net Assets:
Beginning of Period		421,307			304,421
End of Period	$	378,120		$	421,307

The accompanying notes are an integral part of the consolidated financial statements.
54

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Global Strategist Portfolio

Consolidated Statements of Changes in Net Assets (cont'd)	Year Ended September 30, 2020 (000)			Year Ended September 30, 2019 (000)
(1) Capital Share Transactions:
Class I:
Shares Subscribed		393			397
Shares Issued on Distributions Reinvested		65			535
Shares Redeemed		(2,066	)		(903	)
Net Increase (Decrease) in Class I Shares Outstanding		(1,608	)		29
Class A:
Shares Subscribed		140			585
Shares Issued on Distributions Reinvested		184			1,788
Shares Redeemed		(2,489	)		(2,601	)
Net Decrease in Class A Shares Outstanding		(2,165	)		(228	)
Class L:
Shares Exchanged		23			29
Shares Issued on Distributions Reinvested		14			137
Shares Redeemed		(103	)		(340	)
Net Decrease in Class L Shares Outstanding		(66	)		(174	)
Class C:
Shares Subscribed		14			44
Shares Issued on Distributions Reinvested		2			16
Shares Redeemed		(50	)		(46	)
Net Increase (Decrease) in Class C Shares Outstanding		(34	)		14
Class IS:
Shares Subscribed		5			9,774
Shares Issued on Distributions Reinvested		177			1
Shares Redeemed		(70	)		(5	)
Net Increase in Class IS Shares Outstanding		112			9,770

The accompanying notes are an integral part of the consolidated financial statements.
55

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Financial Highlights

Global Strategist Portfolio

	Class I
	Year Ended September 30,
Selected Per Share Data and Ratios	2020			2019			2018			2017			2016(1)(2)
Net Asset Value, Beginning of Period	$	15.45		$	17.05		$	17.48		$	15.79		$	14.58
Income from Investment Operations:
Net Investment Income(3)		0.17			0.27			0.33			0.30			0.28
Net Realized and Unrealized Gain		0.74			0.17			0.35			1.57			0.95
Total from Investment Operations		0.91			0.44			0.68			1.87			1.23
Distributions from and/or in Excess of:
Net Investment Income		(0.03	)		(0.58	)		(0.21	)		(0.18	)		—
Net Realized Gain		(0.25	)		(1.46	)		(0.90	)		—			(0.02	)
Total Distributions		(0.28	)		(2.04	)		(1.11	)		(0.18	)		(0.02	)
Net Asset Value, End of Period	$	16.08		$	15.45		$	17.05		$	17.48		$	15.79
Total Return(4)		5.93	%		3.74	%		3.94	%		11.98	%		8.42	%(5)
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	34,031		$	57,532		$	62,998		$	69,017		$	74,158
Ratio of Expenses Before Expense Limitation		0.84	%		0.84	%		0.85	%		0.85	%		0.81	%
Ratio of Expenses After Expense Limitation		0.72	%(6)		0.72	%(6)		0.73	%(6)		0.72	%(6)		0.68	%(6)
Ratio of Net Investment Income		1.14	%(6)		1.80	%(6)		1.95	%(6)		1.87	%(6)		1.84	%(6)
Ratio of Rebate from Morgan Stanley Affiliates		0.02	%		0.02	%		0.01	%		0.02	%		0.01	%
Portfolio Turnover Rate		109	%		117	%		132	%		176	%		103	%

(1)  Reflects prior period custodian out-of-pocket expenses that were reimbursed in September 2016. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class I shares. The Ratio of Expenses After Expense Limitation would have been 0.05% higher and the Ratio of Net Investment Income would have been 0.05% lower had the custodian not reimbursed the Fund.

(2)  Not consolidated.

(3)  Per share amount is based on average shares outstanding.

(4)  Calculated based on the net asset value as of the last business day of the period.

(5)  Performance was positively impacted by approximately 0.21% due to the receipt of proceeds from the settlement of class action suits involving the Fund's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class I shares would have been approximately 8.21%.

(6)  The Ratio of Expenses After Expense Limitation and Ratio of Net Investment Income reflect the rebate of certain Fund expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates."

The accompanying notes are an integral part of the consolidated financial statements.
56

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Financial Highlights

Global Strategist Portfolio

	Class A
	Year Ended September 30,
Selected Per Share Data and Ratios	2020			2019			2018			2017			2016(1)(2)
Net Asset Value, Beginning of Period	$	15.30		$	16.90		$	17.32		$	15.64		$	14.50
Income from Investment Operations:
Net Investment Income(3)		0.13			0.23			0.28			0.25			0.23
Net Realized and Unrealized Gain		0.73			0.15			0.35			1.56			0.93
Total from Investment Operations		0.86			0.38			0.63			1.81			1.16
Distributions from and/or in Excess of:
Net Investment Income		—			(0.52	)		(0.15	)		(0.13	)		—
Net Realized Gain		(0.25	)		(1.46	)		(0.90	)		—			(0.02	)
Total Distributions		(0.25	)		(1.98	)		(1.05	)		(0.13	)		(0.02	)
Net Asset Value, End of Period	$	15.91		$	15.30		$	16.90		$	17.32		$	15.64
Total Return(4)		5.65	%		3.38	%		3.68	%		11.64	%		7.98	%(5)
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	170,643		$	197,271		$	221,707		$	247,483		$	259,999
Ratio of Expenses Before Expense Limitation		1.08	%		1.09	%		1.09	%		1.12	%		1.11	%
Ratio of Expenses After Expense Limitation		1.02	%(6)		1.03	%(6)		1.03	%(6)		1.05	%(6)		0.99	%(6)
Ratio of Net Investment Income		0.87	%(6)		1.49	%(6)		1.66	%(6)		1.52	%(6)		1.56	%(6)
Ratio of Rebate from Morgan Stanley Affiliates		0.02	%		0.02	%		0.01	%		0.02	%		0.01	%
Portfolio Turnover Rate		109	%		117	%		132	%		176	%		103	%

(1)  Reflects prior period custodian out-of-pocket expenses that were reimbursed in September 2016. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class A shares. The Ratio of Expenses After Expense Limitation would have been 0.07% higher and the Ratio of Net Investment Income would have been 0.07% lower had the custodian not reimbursed the Fund.

(2)  Not consolidated.

(3)  Per share amount is based on average shares outstanding.

(4)  Calculated based on the net asset value which does not reflect sales charges, if applicable, as of the last business day of the period.

(5)  Performance was positively impacted by approximately 0.27% due to the receipt of proceeds from the settlement of class action suits involving the Fund's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class A shares would have been approximately 7.71%.

(6)  The Ratio of Expenses After Expense Limitation and Ratio of Net Investment Income reflect the rebate of certain Fund expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates."

The accompanying notes are an integral part of the consolidated financial statements.
57

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Financial Highlights

Global Strategist Portfolio

	Class L
	Year Ended September 30,
Selected Per Share Data and Ratios	2020			2019			2018			2017			2016(1)(2)
Net Asset Value, Beginning of Period	$	15.15		$	16.73		$	17.15		$	15.47		$	14.41
Income from Investment Operations:
Net Investment Income(3)		0.05			0.15			0.19			0.16			0.15
Net Realized and Unrealized Gain		0.72			0.16			0.34			1.55			0.93
Total from Investment Operations		0.77			0.31			0.53			1.71			1.08
Distributions from and/or in Excess of:
Net Investment Income		—			(0.43	)		(0.05	)		(0.03	)		—
Net Realized Gain		(0.25	)		(1.46	)		(0.90	)		—			(0.02	)
Total Distributions		(0.25	)		(1.89	)		(0.95	)		(0.03	)		(0.02	)
Net Asset Value, End of Period	$	15.67		$	15.15		$	16.73		$	17.15		$	15.47
Total Return(4)		5.10	%		2.87	%		3.13	%		11.07	%		7.47	%(5)
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	12,773		$	13,356		$	17,665		$	20,605		$	23,051
Ratio of Expenses Before Expense Limitation		1.60	%		1.58	%		1.58	%		1.66	%		1.64	%
Ratio of Expenses After Expense Limitation		1.54	%(6)		1.53	%(6)		1.52	%(6)		1.57	%(6)		1.52	%(6)
Ratio of Net Investment Income		0.36	%(6)		0.97	%(6)		1.12	%(6)		1.00	%(6)		1.03	%(6)
Ratio of Rebate from Morgan Stanley Affiliates		0.02	%		0.02	%		0.01	%		0.02	%		0.01	%
Portfolio Turnover Rate		109	%		117	%		132	%		176	%		103	%

(1)  Reflects prior period custodian out-of-pocket expenses that were reimbursed in September 2016. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class L shares. The Ratio of Expenses After Expense Limitation would have been 0.06% higher and the Ratio of Net Investment Income would have been 0.06% lower had the custodian not reimbursed the Fund.

(2)  Not consolidated.

(3)  Per share amount is based on average shares outstanding.

(4)  Calculated based on the net asset value as of the last business day of the period.

(5)  Performance was positively impacted by approximately 0.20% due to the receipt of proceeds from the settlement of class action suits involving the Fund's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class L shares would have been approximately 7.27%.

(6)  The Ratio of Expenses After Expense Limitation and Ratio of Net Investment Income reflect the rebate of certain Fund expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates."

The accompanying notes are an integral part of the consolidated financial statements.
58

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Financial Highlights

Global Strategist Portfolio

	Class C
	Year Ended September 30,
Selected Per Share Data and Ratios	2020			2019			2018			2017			2016(1)(2)
Net Asset Value, Beginning of Period	$	15.02		$	16.65		$	17.08		$	15.42		$	14.41
Income from Investment Operations:
Net Investment Income(3)		0.01			0.11			0.21			0.11			0.10
Net Realized and Unrealized Gain		0.71			0.15			0.27			1.55			0.93
Total from Investment Operations		0.72			0.26			0.48			1.66			1.03
Distributions from and/or in Excess of:
Net Investment Income		—			(0.43	)		(0.01	)		—			—
Net Realized Gain		(0.25	)		(1.46	)		(0.90	)		—			(0.02	)
Total Distributions		(0.25	)		(1.89	)		(0.91	)		—			(0.02	)
Net Asset Value, End of Period	$	15.49		$	15.02		$	16.65		$	17.08		$	15.42
Total Return(4)		4.81	%		2.55	%		2.83	%		10.77	%		7.13	%(5)
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	1,435		$	1,906		$	1,885		$	1,386		$	1,613
Ratio of Expenses Before Expense Limitation		1.98	%		1.93	%		1.99	%		2.02	%		1.94	%
Ratio of Expenses After Expense Limitation		1.82	%(6)		1.82	%(6)		1.83	%(6)		1.82	%(6)		1.81	%(6)
Ratio of Net Investment Income		0.07	%(6)		0.73	%(6)		1.28	%(6)		0.72	%(6)		0.71	%(6)
Ratio of Rebate from Morgan Stanley Affiliates		0.02	%		0.02	%		0.01	%		0.02	%		0.01	%
Portfolio Turnover Rate		109	%		117	%		132	%		176	%		103	%

(1)  Reflects prior period custodian out-of-pocket expenses that were reimbursed in September 2016. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class C shares. The Ratio of Expenses After Expense Limitation would have been 0.02% higher and the Ratio of Net Investment Income would have been 0.02% lower had the custodian not reimbursed the Fund.

(2)  Not consolidated.

(3)  Per share amount is based on average shares outstanding.

(4)  Calculated based on the net asset value which does not reflect sales charges, if applicable, as of the last business day of the period.

(5)  Performance was positively impacted by approximately 0.21% due to the receipt of proceeds from the settlement of class action suits involving the Fund's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class C shares would have been approximately 6.92%.

(6)  The Ratio of Expenses After Expense Limitation and Ratio of Net Investment Income reflect the rebate of certain Fund expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates."

The accompanying notes are an integral part of the consolidated financial statements.
59

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Consolidated Financial Highlights

Global Strategist Portfolio

	Class IS
	Year Ended September 30,
Selected Per Share Data and Ratios	2020			2019			2018			2017			2016(1)(2)
Net Asset Value, Beginning of Period	$	15.46		$	17.06		$	17.49		$	15.79		$	14.59
Income from Investment Operations:
Net Investment Income(3)		0.19			0.27			0.37			0.31			0.26
Net Realized and Unrealized Gain		0.74			0.17			0.31			1.57			0.96
Total from Investment Operations		0.93			0.44			0.68			1.88			1.22
Distributions from and/or in Excess of:
Net Investment Income		(0.04	)		(0.58	)		(0.21	)		(0.18	)		—
Net Realized Gain		(0.25	)		(1.46	)		(0.90	)		—			(0.02	)
Total Distributions		(0.29	)		(2.04	)		(1.11	)		(0.18	)		(0.02	)
Net Asset Value, End of Period	$	16.10		$	15.46		$	17.06		$	17.49		$	15.79
Total Return(4)		6.02	%		3.77	%		3.98	%		12.08	%		8.42	%(5)
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	159,238		$	151,242		$	166		$	137		$	143
Ratio of Expenses Before Expense Limitation		0.75	%		0.75	%		1.95	%		2.17	%		5.44	%
Ratio of Expenses After Expense Limitation		0.69	%(6)		0.69	%(6)		0.70	%(6)		0.69	%(6)		0.70	%(6)
Ratio of Net Investment Income		1.21	%(6)		1.76	%(6)		2.13	%(6)		1.88	%(6)		1.68	%(6)
Ratio of Rebate from Morgan Stanley Affiliates		0.02	%		0.02	%		0.01	%		0.02	%		0.01	%
Portfolio Turnover Rate		109	%		117	%		132	%		176	%		103	%

(1)  Reflects prior period custodian out-of-pocket expenses that were reimbursed in September 2016. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class IS shares. The Ratio of Expenses After Expense Limitation and the Ratio of Net Investment Income would be unchanged as the reimbursement of custodian fees was offset against expense waivers/reimbursements with no impact to net expenses or net investment income.

(2)  Not consolidated.

(3)  Per share amount is based on average shares outstanding.

(4)  Calculated based on the net asset value as of the last business day of the period.

(5)  Performance was positively impacted by approximately 0.35% due to the receipt of proceeds from the settlement of class action suits involving the Fund's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class IS shares would have been approximately 8.07%.

(6)  The Ratio of Expenses After Expense Limitation and Ratio of Net Investment Income reflect the rebate of certain Fund expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates."

The accompanying notes are an integral part of the consolidated financial statements.
60

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Consolidated Financial Statements

Morgan Stanley Institutional Fund Trust ("Trust") is registered under the Investment Company Act of 1940, as amended (the "Act"), as an open-end management investment company. The Trust is comprised of twelve separate, active funds (individually referred to as a "Fund," collectively as the "Funds"). The Trust applies investment company accounting and reporting guidance. All Funds are considered diversified for purposes of the Act.

The accompanying consolidated financial statements relate to the Global Strategist Portfolio. The Fund seeks above-average total return over a market cycle of three to five years. The Fund offers five classes of shares — Class I, Class A, Class L, Class C and Class IS.

The Fund has suspended offering Class L shares for sale to all investors. Class L shareholders of the Fund do not have the option to purchasing additional Class L shares. However, existing Class L shareholders may invest in additional Class L shares through reinvestment of dividends and distributions.

A. Significant Accounting Policies: The following significant accounting policies are in conformity with U.S. generally accepted accounting principles ("GAAP"). Such policies are consistently followed by the Trust in the preparation of its consolidated financial statements. GAAP may require management to make estimates and assumptions that affect the reported amounts and disclosures in the consolidated financial statements. Actual results may differ from those estimates.

The Fund may, consistent with its principal investment strategies, invest up to 25% of its total assets in a wholly-owned subsidiary of the Fund organized as a company under the laws of the Cayman Islands, Global Strategist Cayman Portfolio, Ltd. (the "Subsidiary"). The Subsidiary may invest, directly or indirectly through the use of derivatives, in securities, commodities, commodity-related instruments and other investments, primarily futures, swaps and notes. The Fund is the sole shareholder of the Subsidiary, and it is not currently expected that shares of the Subsidiary will be sold or offered to other investors. The consolidated portfolio of investments and consolidated financial statements include the positions and accounts of the Fund and the Subsidiary. All intercompany accounts and transactions of the Fund and the Subsidiary have been eliminated in consolidation. As of September 30, 2020, the Subsidiary represented approximately $24,146,000 or approximately 6.39% of the total assets of the Fund.

Investments in the Subsidiary are expected to provide the Fund with exposure to the commodity markets within the

limitations of Subchapter M of the Code and recent Internal Revenue Service ("IRS") revenue rulings, which require that a mutual fund receive no more than ten percent of its gross income from such investments in order to receive favorable tax treatment as a regulated investment company ("RIC"). Tax treatment of the income received from the Subsidiary may potentially be affected by changes in legislation, regulations or other legally binding authority, which could affect the character, timing and amount of the Fund's taxable income and distributions. If such changes occur, the Fund may need to significantly change its investment strategy and recognize unrealized gains in order to remain qualified for taxation as a RIC, which could adversely affect the Fund.

In March 2017, the Financial Accounting Standards Board ("FASB") issued an Accounting Standard Update, ASU 2017-08, Receivables-Nonrefundable Fees and Other Costs (Subtopic 310-20), Premium Amortization on Purchased Callable Debt Securities ("ASU 2017-08") which amends the amortization period for certain purchased callable debt securities held at a premium, shortening such period to the earliest call date. ASU 2017-08 does not require any accounting change for debt securities held at a discount; the discount continues to be accreted to maturity. ASU 2017-08 is effective for fiscal years, and interim periods within those fiscal years, beginning after December 15, 2018. The adoption resulted in a change in accounting principle, since the Fund had historically amortized such premiums to maturity for U.S. GAAP. Accordingly, the Fund has adopted ASU 2017-08 to amend the premium amortization period for certain purchased callable debt securities with non-contingent call features to the earliest call date. It is impracticable to evaluate the effect on individual prior periods, therefore the Fund applied the amendments on a modified retrospective basis by recognizing a cumulative effect adjustment that decreased the beginning of period cost of investments and increased the unrealized appreciation on investments of approximately $21,000.

This change in accounting policy has been made to comply with the newly issued accounting standard and had no impact on total accumulated earnings (loss) or the net asset value of the Fund. With respect to the Fund's results of operations, amortization of premium to first call date accelerates amortization with the intent of more closely aligning the recognition of income on such bonds with the economics of the instrument.

In March 2020, FASB issued an Accounting Standard Update, ASU 2020-04, Reference Rate Reform (Topic 848) — Facilitation of the Effects of Reference Rate Reform on

61

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Consolidated Financial Statements (cont'd)

Financial Reporting ("ASU 2020-04"), which provides optional, temporary relief with respect to the financial reporting of contracts subject to certain types of modifications due to the planned discontinuation of the London Interbank Offered Rate ("LIBOR") and other IBOR-based reference rates at the end of 2021. The temporary relief provided by ASU 2020-04 is effective for certain reference rate-related contract modifications that occur during the period from March 12, 2020 through December 31, 2022. Management is evaluating the impact of ASU 2020-04 on the Fund's investments, derivatives, debt and other contracts that will undergo reference rate-related modifications as a result of the reference rate reform.

1.  Security Valuation: (1) Certain portfolio securities may be valued by an outside pricing service/vendor approved by the Trust's Board of Trustees (the "Trustees"). The pricing service/vendor may employ a pricing model that takes into account, among other things, bids, yield spreads and/or other market data and specific security characteristics. Alternatively, if a valuation is not available from an outside pricing service/vendor, and the security trades on an exchange, the security may be valued at its latest reported sale price (or at the exchange official closing price if such exchange reports an official closing price), prior to the time when assets are valued. If there are no sales on a given day and if there is no official exchange closing price for that day, the security is valued at the mean between the last reported bid and asked prices if such bid and asked prices are available in the relevant exchanges. If only bid prices are available then the latest bid price may be used. If Morgan Stanley Investment Management Inc. (the "Adviser") or Morgan Stanley Investment Management Limited ("MSIM Limited") (the "Sub-Adviser"), each a wholly-owned subsidiary of Morgan Stanley, determines that the price provided by the outside pricing service/vendor or exchange does not reflect the security's fair value or is unable to provide a price, prices from brokers or dealers may also be utilized. In these circumstances, the value of the security will be the mean of bid and asked prices obtained from brokers or dealers; (2) an equity portfolio security listed or traded on an exchange is valued at its latest reported sales price (or at the exchange official closing price if such exchange reports an official closing price), and if there were no sales on a given day and if there is no official exchange closing price for that day, the security is valued at the mean between the last reported bid and asked prices if such bid and asked prices

are available on the relevant exchanges. If only bid prices are available then the latest bid price may be used. Listed equity securities not traded on the valuation date with no reported bid and asked prices available on the exchange are valued at the mean between the current bid and asked prices obtained from one or more reputable brokers or dealers. In cases where a security is traded on more than one exchange, the security is valued on the exchange designated as the primary market; (3) all other equity portfolio securities for which over-the-counter ("OTC") market quotations are readily available are valued at the latest reported sales price (or at the market official closing price if such market reports an official closing price), and if there was no trading in the security on a given day and if there is no official closing price from relevant markets for that day, the security is valued at the mean between the last reported bid and asked prices if such bid and asked prices are available on the relevant markets. An unlisted equity security that does not trade on the valuation date and for which bid and asked prices from the relevant markets are unavailable is valued at the mean between the current bid and asked prices obtained from one or more reputable brokers or dealers; (4) futures are valued at the settlement price on the exchange on which they trade or, if a settlement price is unavailable, at the last sale price on the exchange; (5) OTC swaps may be valued by an outside pricing service approved by the Trustees or quotes from a broker or dealer. Swaps cleared on a clearinghouse or exchange may be valued using the closing price provided by the clearinghouse or exchange; (6) when market quotations are not readily available, including circumstances under which the Adviser or the Sub-Adviser determines that the closing price, last sale price or the mean between the last reported bid and asked prices are not reflective of a security's market value, portfolio securities are valued at their fair value as determined in good faith under procedures established by and under the general supervision of the Trustees. Occasionally, developments affecting the closing prices of securities and other assets may occur between the times at which valuations of such securities are determined (that is, close of the foreign market on which the securities trade) and the close of business of the New York Stock Exchange ("NYSE"). If developments occur during such periods that are expected to materially affect the value of such securities, such valuations may be adjusted to reflect the estimated fair value of such securities as of the close of the NYSE, as determined in good faith

62

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Consolidated Financial Statements (cont'd)

by the Trustees or by the Adviser using a pricing service and/or procedures approved by the Trustees; (7) quotations of foreign portfolio securities, other assets and liabilities and forward contracts stated in foreign currency are translated into U.S. dollar equivalents at the prevailing market rates prior to the close of the NYSE; and (8) investments in mutual funds, including the Morgan Stanley Institutional Liquidity Funds, are valued at the net asset value ("NAV") as of the close of each business day.

The Trustees have responsibility for determining in good faith the fair value of the investments, and the Trustees may appoint others, such as the Trust's Adviser or a valuation committee, to assist the Trustees in determining fair value and to make the actual calculations pursuant to the fair valuation methodologies previously approved by the Trustees. Under procedures approved by the Trustees, the Trust's Adviser has formed a Valuation Committee whose members are approved by the Trustees. The Valuation Committee provides administration and oversight of the Trust's valuation policies and procedures, which are reviewed at least annually by the Trustees. These procedures allow the Trust to utilize independent pricing services, quotations from securities and financial instrument dealers and other market sources to determine fair value.

2.  Fair Value Measurement: FASB Accounting Standards Codification^TM ("ASC") 820, "Fair Value Measurement" ("ASC 820"), defines fair value as the value that the Fund would receive to sell an investment or pay to transfer a liability in a timely transaction with an independent buyer in the principal market, or in the absence of a principal market, the most advantageous market for the investment or liability. ASC 820 establishes a three-tier hierarchy to distinguish between (1) inputs that reflect the assumptions market participants would use in valuing an asset or liability developed based on market data obtained from sources independent of the reporting entity (observable inputs) and (2) inputs that reflect the reporting entity's own assumptions about the assumptions market participants would use in valuing an asset or liability developed based on the best information available in the circumstances (unobservable inputs) and to establish classification of fair value measurements for disclosure purposes. Various inputs are used in determining the value

of the Fund's investments. The inputs are summarized in the three broad levels listed below:

•  Level 1 – unadjusted quoted prices in active markets for identical investments

•  Level 2 – other significant observable inputs (including quoted prices for similar investments, interest rates, prepayment speeds, credit risk, etc.)

•  Level 3 – significant unobservable inputs including the Fund's own assumptions in determining the fair value of investments. Factors considered in making this determination may include, but are not limited to, information obtained by contacting the issuer, analysts, or the appropriate stock exchange (for exchange-traded securities), analysis of the issuer's financial statements or other available documents and, if necessary, available information concerning other securities in similar circumstances.

The inputs or methodology used for valuing securities are not necessarily an indication of the risk associated with investing in those securities and the determination of the significance of a particular input to the fair value measurement in its entirety requires judgment and considers factors specific to each security.

The following is a summary of the inputs used to value the Fund's investments as of September 30, 2020:

Investment Type	Level 1 Unadjusted quoted prices (000)		Level 2 Other significant observable inputs (000)			Level 3 Significant unobservable inputs (000)		Total (000)
Assets:
Fixed Income Securities
Agency Adjustable Rate Mortgage	$	—	$	69		$	—	$	69
Agency Fixed Rate Mortgages		—		13,596			—		13,596
Asset-Backed Securities		—		1,780			—		1,780
Collateralized Mortgage Obligations — Agency Collateral Series		—		—	@		—		—	@
Commercial Mortgage-Backed Securities		—		1,946			—		1,946
Corporate Bonds		—		41,325			—		41,325
Mortgages — Other		—		2,187			—		2,187
Sovereign		—		83,364			—		83,364
U.S. Treasury Securities		—		7,603			—		7,603
Total Fixed Income Securities		—		151,870			—		151,870

63

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Consolidated Financial Statements (cont'd)

Investment Type	Level 1 Unadjusted quoted prices (000)		Level 2 Other significant observable inputs (000)		Level 3 Significant unobservable inputs (000)			Total (000)
Common Stocks
Aerospace & Defense	$	4,120	$	517	$	—		$	4,637
Air Freight & Logistics		1,871		499		—			2,370
Airlines		112		24		—			136
Auto Components		1,362		6,238		—			7,600
Automobiles		1,901		7,107		—			9,008
Banks		4,001		3,008		—			7,009
Beverages		1,213		938		—			2,151
Biotechnology		1,603		446		—			2,049
Building Products		2,039		419		—			2,458
Capital Markets		2,073		1,256		—			3,329
Chemicals		1,671		1,702		—			3,373
Commercial Banks		—		2		—			2
Commercial Services & Supplies		1,388		145		—			1,533
Communications Equipment		566		256		—			822
Construction & Engineering		133		355		—			488
Construction Materials		1,101		346		—			1,447
Consumer Finance		376		2		—			378
Containers & Packaging		326		58		—			384
Distributors		75		—		—			75
Diversified Consumer Services		12		—		—			12
Diversified Financial Services		720		382		—			1,102
Diversified Telecommunication Services		1,156		1,035		—			2,191
Electric Utilities		1,358		1,027		—			2,385
Electrical Equipment		1,258		1,170		—			2,428
Electronic Equipment, Instruments & Components		509		128		—			637
Energy Equipment & Services		122		26		—	†		148	†
Entertainment		1,237		141		—			1,378
Equity Real Estate Investment Trusts (REITs)		2,025		530		—			2,555
Food & Staples Retailing		1,376		661		—			2,037
Food Products		787		2,319		—			3,106
Gas Utilities		51		190		—			241
Health Care Equipment & Supplies		2,608		603		—			3,211
Health Care Providers & Services		1,741		265		—			2,006
Health Care Technology		130		—		—			130
Hotels, Restaurants & Leisure		5,309		1,840		—			7,149
Household Durables		11,613		279		—			11,892
Household Products		1,179		507		—			1,686
Independent Power & Renewable Electricity Producers		85		63		—			148
Industrial Conglomerates		2,625		581		—			3,206
Information Technology Services		4,150		250		—			4,400
Insurance		2,495		2,491		—			4,986
Interactive Media & Services		4,041		57		—			4,098

Investment Type	Level 1 Unadjusted quoted prices (000)		Level 2 Other significant observable inputs (000)		Level 3 Significant unobservable inputs (000)			Total (000)
Common Stocks (cont'd)
Internet & Direct Marketing Retail	$	4,029	$	43	$	—		$	4,072
Leisure Products		45		—		—			45
Life Sciences Tools & Services		939		228		—			1,167
Machinery		4,136		934		—			5,070
Marine		—		132		—			132
Media		1,180		195		—			1,375
Metals & Mining		1,298		3,930		—			5,228
Multi-Line Retail		502		233		—			735
Multi-Utilities		664		580		—			1,244
Oil, Gas & Consumable Fuels		2,016		1,529		—			3,545
Paper & Forest Products		119		142		—			261
Personal Products		126		1,144		—			1,270
Pharmaceuticals		2,850		4,443		—			7,293
Professional Services		1,450		818		—			2,268
Real Estate Management & Development		65		655		—			720
Road & Rail		3,621		66		—			3,687
Semiconductors & Semiconductor Equipment		3,496		833		—			4,329
Software		6,593		782		—			7,375
Specialty Retail		1,797		242		—			2,039
Tech Hardware, Storage & Peripherals		5,245		—		—			5,245
Textiles, Apparel & Luxury Goods		626		1,465		—			2,091
Thrifts & Mortgage Finance		85		—		—			85
Tobacco		442		505		—			947
Trading Companies & Distributors		816		328		—			1,144
Transportation Infrastructure		—		269		—			269
Water Utilities		64		73		—			137
Wireless Telecommunication Services		177		197		—			374
Total Common Stocks		114,899		57,629		—	†		172,528	†
Preferred Stock
Internet & Direct Marketing Retail		4		—		—			4
Right		5		—		—			5
Warrants		1		—		—			1
Short-Term Investments
Investment Company		44,327		—		—			44,327
U.S. Treasury Security		—		5,154		—			5,154
Total Short-Term Investments		44,327		5,154		—			49,481
Foreign Currency Forward Exchange Contracts		—		1,190		—			1,190
Futures Contracts		392		—		—			392
Interest Rate Swap Agreements		—		716		—			716
Total Return Swap Agreements		—		1,945		—			1,945
Total Assets		159,628		218,504		—	†		378,132	†

64

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Consolidated Financial Statements (cont'd)

Investment Type	Level 1 Unadjusted quoted prices (000)			Level 2 Other significant observable inputs (000)			Level 3 Significant unobservable inputs (000)			Total (000)
Liabilities:
Foreign Currency Forward Exchange Contracts	$	—		$	(759	)	$	—		$	(759	)
Futures Contracts		(159	)		—			—			(159	)
Total Return Swap Agreements		—			(2,455	)		—			(2,455	)
Total Liabilities		(159	)		(3,214	)		—			(3,373	)
Total	$	159,469		$	215,290		$	—	†	$	374,759	†

@  Value is less than $500.

†  Includes one or more securities valued at zero.

Transfers between investment levels may occur as the markets fluctuate and/or the availability of data used in an investment's valuation changes.

Following is a reconciliation of investments in which significant unobservable inputs (Level 3) were used in determining fair value:

	Common Stocks (000)
Beginning Balance	$	—	†
Purchases		—
Sales		—
Amortization of discount		—
Transfers in		—
Transfers out		—
Corporate actions		—
Change in unrealized appreciation (depreciation)		—
Realized gains (losses)		—
Ending Balance	$	—	†
Net change in unrealized appreciation (depreciation) from investments still held as of September 30, 2020	$	—	†

†  Includes one or more securities valued at zero.

3.  Foreign Currency Translation and Foreign Investments: The books and records of the Fund are maintained in U.S. dollars. Foreign currency amounts are translated into U.S. dollars as follows:

–  investments, other assets and liabilities at the prevailing rate of exchange on the valuation date;

–  investment transactions and investment income at the prevailing rates of exchange on the dates of such transactions.

Although the net assets of the Fund are presented at the foreign exchange rates and market values at the close of

the period, the Fund does not isolate that portion of the results of operations arising as a result of changes in the foreign exchange rates from the fluctuations arising from changes in the market prices of securities held at period end. Similarly, the Fund does not isolate the effect of changes in foreign exchange rates from the fluctuations arising from changes in the market prices of securities sold during the period. Accordingly, realized and unrealized foreign currency gains (losses) on investments in securities are included in the reported net realized and unrealized gains (losses) on investment transactions and balances. However, pursuant to U.S. federal income tax regulations, gains and losses from certain foreign currency transactions and the foreign currency portion of gains and losses realized on sales and maturities of foreign denominated debt securities are treated as ordinary income for U.S. federal income tax purposes.

Net realized gains (losses) on foreign currency transactions represent net foreign exchange gains (losses) from foreign currency forward exchange contracts, disposition of foreign currencies, currency gains (losses) realized between the trade and settlement dates on securities transactions, and the difference between the amount of investment income and foreign withholding taxes recorded on the Fund's books and the U.S. dollar equivalent amounts actually received or paid. The change in unrealized currency gains (losses) on foreign currency transactions for the period is reflected in the Consolidated Statement of Operations.

Foreign security and currency transactions may involve certain considerations and risks not typically associated with those of U.S. dollar denominated transactions as a result of, among other factors, fluctuations of exchange rates in relation to the U.S. dollar, the possibility of lower levels of governmental supervision and regulation of foreign securities markets and the possibility of political or economic instability.

Governmental approval for foreign investments may be required in advance of making an investment under certain circumstances in some countries, and the extent of foreign investments in domestic companies may be subject to limitation in other countries. Foreign ownership limitations also may be imposed by the charters of individual companies to prevent, among other concerns, violations of foreign investment limitations. As a result, an additional class of shares (identified as "Foreign" in

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Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Consolidated Financial Statements (cont'd)

the Consolidated Portfolio of Investments) may be created and offered for investment. The "local" and "foreign shares" market values may differ. In the absence of trading of the foreign shares in such markets, the Fund values the foreign shares at the closing exchange price of the local shares.

4.  Derivatives: The Fund may, but is not required to, use derivative instruments for a variety of purposes, including hedging, risk management, portfolio management or to earn income. Derivatives are financial instruments whose value is based, in part, on the value of an underlying asset, interest rate, index or financial instrument. Prevailing interest rates and volatility levels, among other things, also affect the value of derivative instruments. A derivative instrument often has risks similar to its underlying asset and may have additional risks, including imperfect correlation between the value of the derivative and the underlying asset, risks of default by the counterparty to certain transactions, magnification of losses incurred due to changes in the market value of the securities, instruments, indices or interest rates to which the derivative instrument relates, risks that the transactions may not be liquid and risks arising from margin requirements. The use of derivatives involves risks that are different from, and possibly greater than, the risks associated with other portfolio investments. Derivatives may involve the use of highly specialized instruments that require investment techniques and risk analyses different from those associated with other portfolio investments. All of the Fund's holdings, including derivative instruments, are marked-to-market each day with the change in value reflected in unrealized appreciation (depreciation). Upon disposition, a realized gain or loss is recognized.

Certain derivative transactions may give rise to a form of leverage. Leverage magnifies the potential for gain and the risk of loss. Leverage associated with derivative transactions may cause the Fund to liquidate portfolio positions when it may not be advantageous to do so to satisfy its obligations or to meet earmarking or segregation requirements, pursuant to applicable Securities and Exchange Commission ("SEC") rules and regulations, or may cause the Fund to be more volatile than if the Fund had not been leveraged. Although the Adviser seeks to use derivatives to further the Fund's investment objectives, there is no assurance that the use of derivatives will achieve this result.

Following is a description of the derivative instruments and techniques that the Fund used during the period and their associated risks:

Futures: A futures contract is a standardized, exchange-traded agreement to buy or sell a specific quantity of an underlying asset, reference rate or index at a specific price at a specific future time. The value of a futures contract tends to increase and decrease in tandem with the value of the underlying instrument. Depending on the terms of the particular contract, futures contracts are settled through either physical delivery of the underlying instrument on the settlement date or by payment of a cash settlement amount on the settlement date. During the period the futures contract is open, payments are received from or made to the broker based upon changes in the value of the contract (the variation margin). A decision as to whether, when and how to use futures contracts involves the exercise of skill and judgment and even a well-conceived futures transaction may be unsuccessful because of market behavior or unexpected events. In addition to the derivatives risks discussed above, the prices of futures contracts can be highly volatile, using futures contracts can lower total return and the potential loss from futures contracts can exceed the Fund's initial investment in such contracts. No assurance can be given that a liquid market will exist for any particular futures contract at any particular time. There is also the risk of loss by the Fund of margin deposits in the event of bankruptcy of a broker with which the Fund has open positions in the futures contract.

Swaps: The Fund may enter into OTC swap contracts or cleared swap transactions. A swap contract is an agreement between two parties pursuant to which the parties exchange payments at specified dates on the basis of a specified notional amount, with the payments calculated by reference to specified securities, indices, reference rates, currencies or other instruments. Typically swap agreements provide that when the period payment dates for both parties are the same, the payments are made on a net basis (i.e., the two payment streams are netted out, with only the net amount paid by one party to the other). The Fund's obligations or rights under a swap contract entered into on a net basis will generally be equal only to the net amount to be paid or received under the agreement, based on the relative values of the positions held by each party. Cleared swap transactions

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Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Consolidated Financial Statements (cont'd)

may help reduce counterparty credit risk. In a cleared swap, the Fund's ultimate counterparty is a clearinghouse rather than a swap dealer, bank or other financial institution. OTC swap agreements are not entered into or traded on exchanges and often there is no central clearing or guaranty function for OTC swaps. These OTC swaps are often subject to credit risk or the risk of default or non-performance by the counterparty. Both OTC and cleared swaps could result in losses if interest rates, foreign currency exchange rates or other factors are not correctly anticipated by the Fund or if the reference index, security or investments do not perform as expected. During the period swap agreements are open, payments are received from or made to the clearinghouse or counterparty based upon changes in the value of the contract (variation margin). The Dodd-Frank Wall Street Reform and Consumer Protection Act and related regulatory developments require the clearing and exchange-trading of certain standardized swap transactions. Mandatory exchange-trading and clearing is occurring on a phased-in basis.

The Fund's use of swaps during the period included those based on the credit of an underlying security commonly referred to as "credit default swaps." The Fund may be either the buyer or seller in a credit default swap. Where the Fund is the buyer of a credit default swap contract, it would typically be entitled to receive the par (or other agreed-upon) value of a referenced debt obligation from the counterparty to the contract only in the event of a default or similar event by the issuer of the debt obligation. If no default occurs, the Fund would have paid to the counterparty a periodic stream of payments over the term of the contract and received no benefit from the contract. When the Fund is the seller of a credit default swap contract, it typically receives the stream of payments but is obligated to pay an amount equal to the par (or other agreed-upon) value of a referenced debt obligation upon the default or similar event by the issuer of the referenced debt obligation. The use of credit default swaps could result in losses to the Fund if the Adviser fails to correctly evaluate the creditworthiness of the issuer of the referenced debt obligation.

If the Fund is a seller of protection and a credit event occurs, as defined under the terms of that particular swap agreement, the Fund will either (i) pay to the buyer of protection an amount equal to the notional

amount of the swap agreement and take delivery of the referenced obligation, other deliverable obligations or underlying securities comprising the referenced index or (ii) pay a net settlement amount in the form of cash or securities equal to the notional amount of the swap agreement less the recovery value of the referenced obligation or underlying securities comprising the referenced index. If the Fund is a buyer of protection and a credit event occurs, as defined under the terms of that particular swap agreement, the Fund will either (i) receive from the seller of protection an amount equal to the notional amount of the swap agreement and deliver the referenced obligation, other deliverable obligations or underlying securities comprising the referenced index or (ii) receive a net settlement amount in the form of cash or securities equal to the notional amount of the swap agreement less the recovery value of the referenced obligation or underlying securities comprising the referenced index. Recovery values are estimated by market makers considering either industry standard recovery rates or entity specific factors and considerations until a credit event occurs. If a credit event has occurred, the recovery value is determined by a facilitated auction whereby a minimum number of allowable broker bids, together with a specified valuation method, are used to calculate the settlement value. The Fund's maximum risk of loss from counterparty risk, either as the protection seller or as the protection buyer, is the fair value of the swap agreement.

The current credit rating of each individual issuer is listed in the table following the Consolidated Portfolio of Investments and serves as an indicator of the current status of the payment/performance risk of the credit derivative. Alternatively, for credit default swaps on an index of credits, the quoted market prices and current values serve as an indicator of the current status of the payment/performance risk of the credit derivative. Generally, lower credit ratings and increasing market values, in absolute terms, represent a deterioration of the credit and a greater likelihood of an adverse credit event of the issuer.

When the Fund has an unrealized loss on a swap agreement, the Fund has instructed the custodian to pledge cash or liquid securities as collateral with a value approximately equal to the amount of the unrealized loss. Collateral pledges are monitored and subsequently adjusted

67

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Consolidated Financial Statements (cont'd)

if and when the swap valuations fluctuate. If applicable, cash collateral is included with "Due from (to) Broker" in the Consolidated Statement of Assets and Liabilities.

Upfront payments paid or received by the Fund will be reflected as an asset or liability, respectively, in the Consolidated Statement of Assets and Liabilities.

Foreign Currency Forward Exchange Contracts: In connection with its investments in foreign securities, the Fund also entered into contracts with banks, brokers or dealers to purchase or sell securities or foreign currencies at a future date. A foreign currency forward exchange contract ("currency contract") is a negotiated agreement between the contracting parties to exchange a specified amount of currency at a specified future time at a specified rate. The rate can be higher or lower than the spot rate between the currencies that are the subject of the contract. Currency contracts may be used to protect against uncertainty in the level of future foreign currency exchange rates or to gain or modify exposure to a particular currency. In addition, the Fund may use cross currency hedging or proxy hedging with respect to currencies in which the Fund has or expects to have portfolio or currency exposure. Cross currency hedges involve the sale of one currency against the positive exposure to a different currency and may be used for hedging purposes or to establish an active exposure to the exchange rate between any two currencies. To the extent hedged by the use of currency contracts, the precise matching of the currency contract amounts and the value of the securities involved will not generally be possible because the future value of such securities in foreign currencies will change as a consequence of market movements in the value of those securities between the date on which the contract is entered into and the date it matures. Furthermore, such transactions may reduce or preclude the opportunity for gain if the value of the currency should move in the direction opposite to the position taken. There is additional risk to the extent that currency contracts create exposure to currencies in which the Fund's securities are not denominated. Unanticipated changes in currency prices may result in poorer overall performance for the Fund than if it had not entered into such contracts. The use of currency contracts involves the risk of loss from the insolvency or bankruptcy of the counterparty to the contract or the failure of the counterparty to make payments or otherwise comply with the

terms of the contract. A currency contract is marked-to-market daily and the change in market value is recorded by the Fund as unrealized gain or loss. The Fund records realized gains (losses) when the currency contract is closed equal to the difference between the value of the currency contract at the time it was opened and the value at the time it was closed.

FASB ASC 815, "Derivatives and Hedging" ("ASC 815"), is intended to improve financial reporting about derivative instruments by requiring enhanced disclosures to enable investors to better understand how and why the Fund uses derivative instruments, how these derivative instruments are accounted for and their effects on the Fund's financial position and results of operations.

The following tables set forth the fair value of the Fund's derivative contracts by primary risk exposure as of September 30, 2020:

	Asset Derivatives Consolidated Statement of Assets and Liabilities Location	Primary Risk Exposure	Value (000)
Foreign Currency Forward Exchange Contracts	Unrealized Appreciation on Foreign Currency Forward Exchange Contracts	Currency Risk	$	1,190
Futures Contracts	Variation Margin on Futures Contracts	Commodity Risk		26	(a)
Futures Contracts	Variation Margin on Futures Contracts	Equity Risk		283	(a)
Futures Contracts	Variation Margin on Futures Contracts	Interest Rate Risk		83	(a)
Swap Agreements	Variation Margin on Swap Agreements	Interest Rate Risk		645	(a)
Swap Agreements	Unrealized Appreciation on Swap Agreements	Equity Risk		1,945
Swap Agreement	Unrealized Appreciation on Swap Agreement	Interest Rate Risk		71
Total			$	4,243
	Liability Derivatives Consolidated Statement of Assets and Liabilities Location	Primary Risk Exposure	Value (000)
Foreign Currency Forward Exchange Contracts	Unrealized Depreciation on Foreign Currency Forward Exchange Contracts	Currency Risk	$	(759	)
Futures Contract	Variation Margin on Futures Contract	Equity Risk		(50	)(a)
Futures Contracts	Variation Margin on Futures Contracts	Interest Rate Risk		(109	)(a)
Swap Agreements	Unrealized Depreciation on Swap Agreements	Equity Risk		(2,455	)
Total			$	(3,373	)

(a) This amount represents the cumulative appreciation (depreciation) as reported in the Consolidated Portfolio of Investments. The Consolidated Statement of Assets and Liabilities only reflects the current day's net variation margin.

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Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Consolidated Financial Statements (cont'd)

The following tables set forth by primary risk exposure the Fund's realized gains (losses) and change in unrealized appreciation (depreciation) by type of derivative contract for the year ended September 30, 2020 in accordance with ASC 815:

Realized Gain (Loss)
Primary Risk Exposure	Derivative Type	Value (000)
Currency Risk	Foreign Currency Forward Exchange Contracts	$	(2,253	)
Commodity Risk	Futures Contracts		1,920
Equity Risk	Futures Contracts		48
Interest Rate Risk	Futures Contracts		(1,821	)
Credit Risk	Swap Agreements		46
Equity Risk	Swap Agreements		(3,430	)
Interest Rate Risk	Swap Agreements		(40	)
Total		$	(5,530	)
Change in Unrealized Appreciation (Depreciation)
Primary Risk Exposure	Derivative Type	Value (000)
Currency Risk	Foreign Currency Forward Exchange Contracts	$	1,463
Commodity Risk	Futures Contracts		(50	)
Equity Risk	Futures Contracts		683
Interest Rate Risk	Futures Contracts		75
Equity Risk	Swap Agreements		482
Credit Risk	Swap Agreement		(25	)
Interest Rate Risk	Swap Agreements		925
Total		$	3,553

At September 30, 2020, the Fund's derivative assets and liabilities are as follows:

Gross Amounts of Assets and Liabilities Presented in the Consolidated Statement of Assets and Liabilities
Derivatives(b)	Assets(c) (000)		Liabilities(c) (000)
Foreign Currency Forward Exchange Contracts	$	1,190	$	(759	)
Swap Agreements		2,016		(2,455	)
Total	$	3,206	$	(3,214	)

(b) Excludes exchange-traded derivatives.

(c) Absent an event of default or early termination, OTC derivative assets and liabilities are presented gross and not offset in the Consolidated Statement of Assets and Liabilities.

The Fund typically enters into International Swaps and Derivatives Association, Inc. Master Agreements ("ISDA Master Agreements") or similar master agreements (collectively, "Master Agreements") with its contract counterparties for certain OTC derivatives in order to, among other things, reduce its credit risk to counterparties. ISDA Master Agreements include provisions for general obligations, representations, collateral and events of default or termination. Under an ISDA Master Agreement, the Fund typically may offset with the counterparty certain OTC

derivative financial instruments' payables and/or receivables with collateral held and/or posted and create one single net payment (close-out netting) in the event of default, termination and/or potential deterioration in the credit quality of the counterparty. Various Master Agreements govern the terms of certain transactions with counterparties, including transactions such as swap, forward, repurchase and reverse repurchase agreements. These Master Agreements typically attempt to reduce the counterparty risk associated with such transactions by specifying credit protection mechanisms and providing standardization that improves legal certainty. Cross-termination provisions under Master Agreements typically provide that a default in connection with one transaction between the Fund and a counterparty gives the non-defaulting party the right to terminate any other transactions in place with the defaulting party to create one single net payment due to/due from the defaulting party and may be a feature in certain Master Agreements. In the event the Fund exercises its right to terminate a Master Agreement after a counterparty experiences a termination event as defined in the Master Agreement, the return of collateral with market value in excess of the Fund's net liability may be delayed or denied.

The following tables present derivative financial instruments that are subject to enforceable netting arrangements as of September 30, 2020:

Gross Amounts Not Offset in the Consolidated Statement of Assets and Liabilities
Counterparty	Gross Asset Derivatives Presented in the Consolidated Statement of Assets and Liabilities (000)		Financial Instrument (000)			Collateral Received(d) (000)			Net Amount (not less than $0) (000)
Bank of America NA	$	2	$	(2	)	$	—		$	0
Bank of Montreal		1		—			—			1
Bank of New York Mellon		5		—			—			5
Barclays Bank PLC		105		(12	)		—			93
BNP Paribas SA		181		(169	)		(12	)		0
Citibank NA		1		(1	)		—			0
Commonwealth Bank of Australia		2		—			—			2
Credit Suisse International		1		—			—			1
Goldman Sachs International		73		(73	)		—			0
JPMorgan Chase Bank NA		2,192		(1,836	)		(310	)		46
State Street Bank and Trust Co.		1		—			—			1
UBS AG		642		(42	)		—			600
Total	$	3,206	$	(2,135	)	$	(322	)	$	749

69

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Consolidated Financial Statements (cont'd)

Gross Amounts Not Offset in the Consolidated Statement of Assets and Liabilities
Counterparty	Gross Liability Derivatives Presented in the Consolidated Statement of Assets and Liabilities (000)		Financial Instrument (000)			Collateral Pledged(d) (000)			Net Amount (not less than $0) (000)
Australia And New Zealand Banking Group	$	23	$	—		$	—		$	23
Bank of America NA		7		(2	)		—			5
Barclays Bank PLC		77		(12	)		—			65
BNP Paribas SA		169		(169	)		—			0
Citibank NA		114		(1	)		—			113
Goldman Sachs International		498		(73	)		(339	)		86
JPMorgan Chase Bank NA		2,284		(1,836	)		—			448
UBS AG		42		(42	)		—			0
Total	$	3,214	$	(2,135	)	$	(339	)	$	740

(d) In some instances, the actual collateral received may be more than the amount shown here due to overcollateralization.

For the year ended September 30, 2020, the approximate average monthly amount outstanding for each derivative type is as follows:

Foreign Currency Forward Exchange Contracts:
Average monthly principal amount	$	131,655,000
Futures Contracts:
Average monthly notional value	$	121,058,000
Swap Agreements:
Average monthly notional amount	$	62,217,000

5.  When-Issued/Delayed Delivery Securities: The Fund purchases and sells when-issued and delayed delivery securities. Securities purchased on a when-issued or delayed delivery basis are purchased for delivery beyond the normal settlement date at a stated price and yield, and no income accrues to the Fund on such securities prior to delivery date. Payment and delivery for when-issued and delayed delivery securities can take place a month or more after the date of the transaction. When the Fund enters into a purchase transaction on a when-issued or delayed delivery basis, securities are available for collateral in an amount at least equal in value to the Fund's commitments to purchase such securities. Purchasing securities on a when-issued or delayed delivery basis may involve a risk that the market price at the time of delivery may be lower than the agreed upon purchase price, in which case there could be an unrealized loss at the time of delivery. Purchasing investments on a when-issued or delayed delivery basis may be considered a form of leverage which may

increase the impact that gains (losses) may have on the Fund.

6.  Indemnifications: The Trust enters into contracts that contain a variety of indemnifications. The Trust's maximum exposure under these arrangements is unknown. However, the Trust has not had prior claims or losses pursuant to these contracts and expects the risk of loss to be remote.

7.  Dividends and Distributions to Shareholders: Dividends and distributions to shareholders are recorded on the ex-dividend date. Dividends from net investment income, if any, are declared and paid annually. Net realized capital gains, if any, are distributed at least annually.

8.  Security Transactions, Income and Expenses: Security transactions are accounted for on the trade date (date the order to buy or sell is executed). Realized gains and losses on the sale of investment securities are determined on the specific identified cost method. Dividend income and other distributions are recorded on the ex-dividend date (except for certain foreign dividends which may be recorded as soon as the Fund is informed of such dividends) net of applicable withholding taxes. Interest income is recognized on the accrual basis except where collection is in doubt. Discounts are accreted and premiums are amortized over the life of the respective securities. Most expenses of the Trust can be directly attributed to a particular Fund. Expenses which cannot be directly attributed are apportioned among the Funds based upon relative net assets or other appropriate methods. Income, expenses (other than class specific expenses — distribution and shareholder services, transfer agency and sub transfer agency fees) and realized and unrealized gains or losses are allocated to each class of shares based upon their relative net assets.

The Fund owns shares of real estate investment trusts ("REITs") which report information on the source of their distributions annually in the following calendar year. A portion of distributions received from REITs during the year is estimated to be a return of capital and is recorded as a reduction of their cost.

B. Advisory/Sub-Advisory Fees: The Adviser, a wholly-owned subsidiary of Morgan Stanley, provides the Fund with advisory services under the terms of an Investment Advisory

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Morgan Stanley Institutional Fund Trust

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Notes to Consolidated Financial Statements (cont'd)

Agreement, paid quarterly, at an annual rate of 0.45% of the average daily net assets of the Fund.

The Adviser has agreed to reduce its advisory fee and/or reimburse the Fund so that total annual Fund operating expenses, excluding certain investment related expenses, taxes, interest and other extraordinary expenses (including litigation), will not exceed 0.74% for Class I shares, 1.09% for Class A shares, 1.59% for Class L shares, 1.84% for Class C shares and 0.71% for Class IS shares. The fee waivers and/or expense reimbursements will continue for at least one year from the date of the Fund's prospectus or until such time as the Trustees act to discontinue all or a portion of such waivers and/or reimbursements when they deem such action is appropriate. For the year ended September 30, 2020, approximately $144,000 of advisory fees were waived and approximately $36,000 of other expenses were reimbursed by the Adviser pursuant to this arrangement.

The Adviser has entered into a Sub-Advisory Agreement with the Sub-Adviser, a wholly-owned subsidiary of Morgan Stanley. The Sub-Adviser provides the Fund with advisory services subject to the overall supervision of the Adviser and the Fund's Officers and Trustees. The Adviser pays the Sub-Adviser on a monthly basis a portion of the net advisory fees the Adviser receives from the Fund.

The Adviser provides investment advisory services to the Subsidiary pursuant to the Subsidiary Investment Management Agreement (the "Agreement"). Under the Agreement, the Subsidiary will pay the Adviser at the end of each fiscal quarter, calculated by applying a quarterly rate, based on the annual rate of 0.05%, to the average daily net assets of the Subsidiary.

The Adviser has agreed to waive its advisory fees by the amount of advisory fees it receives from the Subsidiary.

C. Administration Fees: The Adviser also serves as Administrator to the Trust and provides administrative services pursuant to an Administration Agreement for an annual fee, accrued daily and paid monthly, of 0.08% of the Fund's average daily net assets. Under a Sub-Administration Agreement between the Administrator and State Street Bank and Trust Company ("State Street"), State Street provides certain administrative services to the Trust. For such services, the Administrator pays State Street a portion of the fee the Administrator receives from the Fund.

D. Distribution and Shareholder Services Fees: Morgan Stanley Distribution, Inc. ("MSDI" or the "Distributor"), a wholly-owned subsidiary of the Adviser, and an indirect subsidiary of Morgan Stanley, serves as the Trust's Distributor of Fund shares pursuant to a Distribution Agreement. The Trust has adopted a Shareholder Services Plan with respect to Class A shares pursuant to Rule 12b-1 under the Act. Under the Shareholder Services Plan, the Fund pays the Distributor a shareholder services fee, accrued daily and paid monthly, at an annual rate of 0.25% of the Fund's average daily net assets attributable to Class A shares.

The Trust has adopted a Distribution and Shareholder Services Plan with respect to Class L shares pursuant to Rule 12b-1 under the Act. Under the Distribution and Shareholder Services Plan, the Fund pays the Distributor a distribution fee, accrued daily and paid monthly, at an annual rate of 0.50% and a shareholder services fee, accrued daily and paid monthly, at an annual rate of 0.25% of the Fund's average daily net assets attributable to Class L shares.

The Trust has adopted a Distribution and Shareholder Services Plan with respect to Class C shares pursuant to Rule 12b-1 under the Act. Under the Distribution and Shareholder Services Plan, the Fund pays the Distributor a distribution fee, accrued daily and paid monthly, at an annual rate of 0.75% and a shareholder services fee, accrued daily and paid monthly, at an annual rate of 0.25% of the Fund's average daily net assets attributable to Class C shares.

The distribution and shareholder services fees are used to support the expenses associated with servicing and maintaining accounts. The Distributor may compensate other parties for providing shareholder support services to investors who purchase Class A, Class L and Class C shares.

E. Dividend Disbursing and Transfer Agent: The Trust's dividend disbursing and transfer agent is DST Asset Manager Solutions, Inc. ("DST"). Pursuant to a Transfer Agency Agreement, the Trust pays DST a fee based on the number of classes, accounts and transactions relating to the Funds of the Trust.

F. Custodian Fees: State Street (the "Custodian") also serves as Custodian for the Trust in accordance with a Custodian Agreement. The Custodian holds cash, securities and other assets of the Trust as required by the Act. Custody fees

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Morgan Stanley Institutional Fund Trust

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Notes to Consolidated Financial Statements (cont'd)

are payable monthly based on assets held in custody, investment purchases and sales activity and account maintenance fees, plus reimbursement for certain out-of-pocket expenses.

G. Security Transactions and Transactions with Affiliates: For the year ended September 30, 2020, purchases and sales of investment securities for the Fund, other than long-term U.S. Government securities and short-term investments were approximately $215,111,000 and $267,372,000, respectively. For the year ended September 30, 2020, purchases and sales of long-term U.S. Government securities were approximately $169,877,000 and $180,314,000, respectively.

The Fund invests in the Institutional Class of the Morgan Stanley Institutional Liquidity Funds — Government Portfolio (the "Liquidity Funds"), an open-end management investment company managed by the Adviser. Advisory fees paid by the Fund are reduced by an amount equal to its pro-rata share of the advisory and administration fees paid by the Fund due to its investment in the Liquidity Funds. For the year ended September 30, 2020, advisory fees paid were reduced by approximately $94,000 relating to the Fund's investment in the Liquidity Funds.

A summary of the Fund's transactions in shares of affiliated investments during the year ended September 30, 2020 is as follows:

Affiliated Investment Company	Value September 30, 2019 (000)		Purchases at Cost (000)		Proceeds from Sales (000)		Dividend Income (000)
Liquidity Funds	$	50,100	$	241,604	$	247,377	$	417

Affiliated Investment Company (cont'd)	Realized Gain (Loss) (000)		Change in Unrealized Appreciation (Depreciation) (000)		Value September 30, 2020 (000)
Liquidity Funds	$	—	$	—	$	44,327

The Fund is permitted to purchase and sell securities ("cross-trade") from and to other Morgan Stanley funds as well as other funds and client accounts for which the Adviser or an affiliate of the Adviser serves as investment adviser, pursuant to procedures approved by the Trustees in compliance with Rule 17a-7 under the Act (the "Rule"). Each cross-trade is executed at the current market price in compliance with provisions of the Rule. For the year ended September 30, 2020, the Fund did not engage in any cross-trade transactions.

The Fund has an unfunded Deferred Compensation Plan (the "Compensation Plan"), which allows each independent Trustee to defer payment of all, or a portion, of the fees he or she receives for serving on the Board of Trustees. Each eligible

Trustee generally may elect to have the deferred amounts credited with a return equal to the total return on one or more of the Morgan Stanley funds that are offered as investment options under the Compensation Plan. Appreciation/depreciation and distributions received from these investments are recorded with an offsetting increase/decrease in the deferred compensation obligation and do not affect the NAV of the Fund.

H. Federal Income Taxes: It is the Fund's intention to continue to qualify as a regulated investment company and distribute all of its taxable and tax-exempt income. Accordingly, no provision for federal income taxes is required in the consolidated financial statements.

The Fund may be subject to taxes imposed by countries in which it invests. Such taxes are generally based on income and/or capital gains earned or repatriated. Taxes are accrued based on net investment income, net realized gains and net unrealized appreciation as such income and/or gains are earned. Taxes may also be based on transactions in foreign currency and are accrued based on the value of investments denominated in such currency.

FASB ASC 740-10, "Income Taxes — Overall", sets forth a minimum threshold for consolidated financial statement recognition of the benefit of a tax position taken or expected to be taken in a tax return. Management has concluded that there are no significant uncertain tax positions that would require recognition in the consolidated financial statements. If applicable, the Fund recognizes interest accrued related to unrecognized tax benefits in "Interest Expense" and penalties in "Other Expenses" in the Consolidated Statement of Operations. The Fund files tax returns with the U.S. Internal Revenue Service, New York and various states. Generally, each of the tax years in the four-year period ended September 30, 2020 remains subject to examination by taxing authorities.

The tax character of distributions paid may differ from the character of distributions shown for GAAP purposes due to short-term capital gains being treated as ordinary income for tax purposes. The tax character of distributions paid during fiscal years 2020 and 2019 was as follows:

2020 Distributions Paid From:				2019 Distributions Paid From:
Ordinary Income (000)		Long-Term Capital Gain (000)		Ordinary Income (000)		Long-Term Capital Gain (000)
$	5,926	$	1,055	$	9,365	$	25,784

72

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Consolidated Financial Statements (cont'd)

The amount and character of income and gains to be distributed are determined in accordance with income tax regulations which may differ from GAAP. These book/tax differences are either considered temporary or permanent in nature.

Temporary differences are attributable to differing book and tax treatments for the timing of the recognition of gains (losses) on certain investment transactions and the timing of the deductibility of certain expenses.

Permanent differences, primarily due to wash sale adjustments, resulted in the following reclassifications among the components of net assets at September 30, 2020:

Total Distributable Earnings (000)		Paid-in- Capital (000)
$	2	$	(2	)

At September 30, 2020, the components of distributable earnings for the Fund on a tax basis were as follows:

Undistributed Ordinary Income (000)		Undistributed Long-Term Capital Gain (000)
$	4,953	$	—

I. Credit Facility: The Trust and other Morgan Stanley funds participated in a $300,000,000 committed, unsecured revolving line of credit facility (the "Facility") with State Street. This Facility is to be used for temporary emergency purposes or funding of shareholder redemption requests. The interest rate on borrowings is based on the federal funds rate or 1 month LIBOR rate plus a spread. The Facility also has a commitment fee of 0.25% per annum based on the unused portion of the Facility. During the year ended September 30, 2020, the Fund did not have any borrowings under the Facility.

J. Other: At September 30, 2020, the Fund had record owners of 10% or greater. Investment activities of these shareholders could have a material impact on the Fund. The aggregate percentage of such owners was 74.8%.

K. Market Risk: Certain impacts to public health conditions particular to the coronavirus (COVID-19) outbreak could impact the operations and financial performance of certain of the Fund's investments. The extent of the impact to the financial performance of the Fund's investments will depend on future developments, including (i) the duration and spread of the outbreak, (ii) the restrictions and advisories, (iii) the effects on the financial markets, and (iv) the effects on the economy overall, all of which are highly uncertain and cannot be predicted.

If the financial performance of the Fund's investments is impacted because of these factors for an extended period, the Fund's investment results may be adversely affected.

L. LIBOR Risk: The Fund's investments, payment obligations and financing terms may be based on floating rates, such as London Interbank Offer Rate ("LIBOR"), Euro Interbank Offered Rate and other similar types of reference rates (each, a "Reference Rate"). These Reference Rates are generally intended to represent the rate at which contributing banks may obtain short-term borrowings from each other within certain financial markets. On July 27, 2017, the Chief Executive of the UK Financial Conduct Authority ("FCA"), which regulates LIBOR, announced that the FCA will no longer persuade nor require banks to submit rates for the calculation of LIBOR and certain other Reference Rates after 2021. Such announcement indicates that the continuation of LIBOR and other Reference Rates on the current basis cannot and will not be guaranteed after the end of 2021. This announcement and any additional regulatory or market changes may have an adverse impact on the Fund or its investments.

In advance of 2022, regulators and market participants are currently engaged in identifying successor Reference Rates ("Alternative Reference Rates"). Additionally, prior to the end of 2021, it is expected that market participants will focus on the transition mechanisms by which the Reference Rates in existing contracts or instruments may be amended, whether through marketwide protocols, fallback contractual provisions, bespoke negotiations or amendments or otherwise. Nonetheless, the termination of certain Reference Rates presents risks to the Fund. At this time, it is not possible to completely identify or predict the effect of any such changes, any establishment of Alternative Reference Rates or any other reforms to Reference Rates that may be enacted in the UK or elsewhere. The elimination of a Reference Rate or any other changes or reforms to the determination or supervision of Reference Rates could have an adverse impact on the market for or value of any securities or payments linked to those Reference Rates and other financial obligations held by the Fund or on its overall financial condition or results of operations.

73

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Report of Independent Registered Public Accounting Firm

To the Shareholders and Board of Trustees of
Morgan Stanley Institutional Fund Trust —
Global Strategist Portfolio

Opinion on the Financial Statements

We have audited the accompanying consolidated statement of assets and liabilities of Global Strategist Portfolio (the "Fund") (one of the funds constituting Morgan Stanley Institutional Fund Trust (the "Trust")), including the consolidated portfolio of investments, as of September 30, 2020, and the related consolidated statement of operations for the year then ended, the consolidated statements of changes in net assets for each of the two years in the period then ended, the consolidated financial highlights for each of the five years in the period then ended and the related notes (collectively referred to as the "financial statements"). In our opinion, the financial statements present fairly, in all material respects, the consolidated financial position of the Fund (one of the funds constituting Morgan Stanley Institutional Fund Trust) at September 30, 2020, the consolidated results of its operations for the year then ended, the consolidated changes in its net assets for each of the two years in the period then ended and its consolidated financial highlights for each of the five years in the period then ended, in conformity with U.S. generally accepted accounting principles.

Basis for Opinion

These financial statements are the responsibility of the Trust's management. Our responsibility is to express an opinion on the Fund's financial statements based on our audits. We are a public accounting firm registered with the Public Company Accounting Oversight Board (United States) ("PCAOB") and are required to be independent with respect to the Trust in accordance with the U.S. federal securities law and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB.

We conducted our audits in accordance with the standards of the PCAOB. Those standards require that we plan and perform the audit to obtain reasonable assurance about whether the financial statements are free of material misstatement, whether due to error or fraud. The Trust is not required to have, nor were we engaged to perform, an audit of the Trust's internal control over financial reporting. As part of our audits we are required to obtain an understanding of internal control over financial reporting but not for the purpose of expressing an opinion on the effectiveness of the Trust's internal control over financial reporting. Accordingly, we express no such opinion.

Our audits included performing procedures to assess the risks of material misstatement of the financial statements, whether due to error or fraud, and performing procedures that respond to those risks. Such procedures included examining, on a test basis, evidence regarding the amounts and disclosures in the financial statements. Our procedures included confirmation of securities owned as of September 30, 2020 by correspondence with the custodian and brokers or by other appropriate auditing procedures where replies from brokers were not received. Our audits also included evaluating the accounting principles used and significant estimates made by management, as well as evaluating the overall presentation of the financial statements. We believe that our audits provide a reasonable basis for our opinion.

We have served as the auditor of one or more Morgan Stanley investment companies since 2000.
Boston, Massachusetts
November 24, 2020

74

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Advisory Agreement Approval (unaudited)

Nature, Extent and Quality of Services

The Board reviewed and considered the nature and extent of the investment advisory services provided by the Adviser under the advisory agreement, including portfolio management, investment research and equity and fixed income securities trading. The Board reviewed similar information and factors regarding the Sub-Adviser, to the extent applicable. The Board also reviewed and considered the nature and extent of the non-advisory, administrative services provided by the Administrator under the administration agreement, including accounting, operations, clerical, bookkeeping, compliance, business management and planning, legal services and the provision of supplies, office space and utilities at the Adviser's expense. The Board also considered the Adviser's investment in personnel and infrastructure that benefits the Fund. (The Adviser, Sub-Adviser and Administrator together are referred to as the "Adviser" and the advisory, sub-advisory and administration agreements together are referred to as the "Management Agreement.") The Board also considered that the Adviser serves a variety of other investment advisory clients and has experience overseeing service providers. The Board also compared the nature of the services provided by the Adviser with similar services provided by non-affiliated advisers as prepared by Broadridge Financial Solutions, Inc. ("Broadridge").

The Board reviewed and considered the qualifications of the portfolio managers, the senior administrative managers and other key personnel of the Adviser who provide the advisory and administrative services to the Fund. The Board determined that the Adviser's portfolio managers and key personnel are well qualified by education and/or training and experience to perform the services in an efficient and professional manner. The Board concluded that the nature and extent of the advisory and administrative services provided were necessary and appropriate for the conduct of the business and investment activities of the Fund and supported its decision to approve the Management Agreement.

Performance, Fees and Expenses of the Fund

The Board reviewed the performance, fees and expenses of the Fund compared to its peers, as prepared by Broadridge, and to appropriate benchmarks where applicable. The Board discussed with the Adviser the performance goals and the actual results achieved in managing the Fund. When considering a fund's performance, the Board and the Adviser place emphasis on trends and longer-term returns (focusing on one-year, three-year and five-year performance, as of December 31, 2019, or since inception, as applicable). When a fund underperforms its benchmark and/or its peer group average, the Board and the Adviser discuss the causes of such underperformance and, where necessary, they discuss specific changes to investment strategy or investment personnel. The Board noted that the Fund's performance was better than its peer group average for the one-, three- and five-year periods. The Board discussed with the Adviser the level of the advisory and administration fees (together, the "management fee") for this Fund relative to comparable funds and/or other accounts advised by the Adviser and/or compared to its peers as prepared by Broadridge. In addition to the management fee, the Board also reviewed the Fund's total expense ratio. The Board noted that the Fund's management fee and total expense ratio were lower than its peer group averages. After discussion, the Board concluded that the Fund's performance, management fee and total expense ratio were competitive with its peer group averages.

Economies of Scale

The Board considered the size and growth prospects of the Fund and how that relates to the Fund's total expense ratio and particularly the Fund's management fee rate, which does not include breakpoints. In conjunction with its review of the Adviser's profitability, the Board discussed with the Adviser how a change in assets can affect the efficiency or effectiveness of managing the Fund and whether the management fee level is appropriate relative to current and projected asset levels and/or whether the management fee structure reflects economies of scale as asset levels change. The Board has determined that its review of the actual and/or potential economies of scale of the Fund supports its decision to approve the Management Agreement.

Profitability of the Adviser and Affiliates

The Board considered information concerning the costs incurred and profits realized by the Adviser and its affiliates during the last year from their relationship with the Fund and during the last two years from their relationship with the Morgan Stanley Fund Complex and reviewed with the Adviser the cost allocation methodology used to determine the profitability of the Adviser and affiliates. The Board has determined that its review of the analysis of the Adviser's expenses and profitability supports its decision to approve the Management Agreement.

75

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Advisory Agreement Approval (unaudited) (cont'd)

Other Benefits of the Relationship

The Board considered other direct and indirect benefits to the Adviser and/or its affiliates derived from their relationship with the Fund and other funds advised by the Adviser. These benefits may include, among other things, fees for trading, distribution and/or shareholder servicing and for transaction processing and reporting platforms used by securities lending agents, and research received by the Adviser generated from commission dollars spent on funds' portfolio trading. The Board reviewed with the Adviser these arrangements and the reasonableness of the Adviser's costs relative to the services performed. The Board has determined that its review of the other benefits received by the Adviser or its affiliates supports its decision to approve the Management Agreement.

Resources of the Adviser and Historical Relationship Between the Fund and the Adviser

The Board considered whether the Adviser is financially sound and has the resources necessary to perform its obligations under the Management Agreement. The Board also reviewed and considered the historical relationship between the Fund and the Adviser, including the organizational structure of the Adviser, the policies and procedures formulated and adopted by the Adviser for managing the Fund's operations and the Board's confidence in the competence and integrity of the senior managers and key personnel of the Adviser. The Board concluded that the Adviser has the financial resources necessary to fulfill its obligations under the Management Agreement and that it is beneficial for the Fund to continue its relationship with the Adviser.

Other Factors and Current Trends

The Board considered the controls and procedures adopted and implemented by the Adviser and monitored by the Fund's Chief Compliance Officer and concluded that the conduct of business by the Adviser indicates a good faith effort on its part to adhere to high ethical standards in the conduct of the Fund's business.

As part of the Board's review, the Board received information from management on the impact of COVID-19 on the firm generally and the Adviser and the Fund in particular including, among other information, the pandemic's current and expected impact on the Fund's performance and operations.

General Conclusion

After considering and weighing all of the above factors, with various written materials and verbal information presented by the Adviser, the Board concluded that it would be in the best interest of the Fund and its shareholders to approve renewal of the Management Agreement for another year. In reaching this conclusion the Board did not give particular weight to any single piece of information or factor referenced above. The Board considered these factors and information over the course of the year and in numerous meetings, some of which were in executive session with only the independent Board members and their counsel present. It is possible that individual Board members may have weighed these factors, and the information presented, differently in reaching their individual decisions to approve the Management Agreement.

76

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Liquidity Risk Management Program (unaudited)

In compliance with Rule 22e-4 under the Investment Company Act of 1940, as amended (the "Liquidity Rule"), the Fund has adopted and implemented a liquidity risk management program (the "Program"), which is reasonably designed to assess and manage the risk that the Fund could not meet requests to redeem shares issued by the Fund without significant dilution of remaining investors' interests in the Fund (i.e., liquidity risk). The Fund's Board of Trustees (the "Board") previously approved the designation of the Liquidity Risk Subcommittee (the "LRS") as Program administrator. The LRS is comprised of representatives from various divisions within Morgan Stanley Investment Management.

At a meeting held on April 22-23, 2020, the Board reviewed a written report prepared by the LRS that addressed the Program's operation and assessed its adequacy, and effectiveness of implementation for the period from December 1, 2018, through December 31, 2019, as required under the Liquidity Rule. The report concluded that the Program operated effectively and was adequately and effectively implemented in all material aspects, and that the relevant controls and safeguards were appropriately designed to enable the LRS to administer the Program in compliance with the Liquidity Rule.

In accordance with the Program, the LRS assessed each Fund's liquidity risk no less frequently than annually taking into consideration certain factors, as applicable, such as (i) investment strategy and liquidity of portfolio investments, (ii) short-term and long-term cash flow projections and (iii) holdings of cash and cash equivalents and borrowing arrangements and other funding sources. Certain factors are considered under both normal and reasonably foreseeable stressed conditions.

Each Fund portfolio investment is classified into one of four liquidity categories, which classification is assessed at least monthly by the LRS. The classification is based on a determination of the number of days it is reasonably expected to take to convert the investment into cash, or sell or dispose of the investment, in current market conditions without significantly changing the market value of the investment. Liquidity classification determinations take into account various market, trading and investment-specific considerations, as well as market depth, and in some cases utilize third-party vendor data.

The Liquidity Rule limits a fund's investments in illiquid investments to 15% of its net assets and requires funds that do not primarily hold assets that are highly liquid investments to determine and maintain a minimum percentage of the fund's net assets to be invested in highly liquid investments (highly liquid investment minimum or "HLIM"). The LRS believes that the Program includes provisions reasonably designed to review, monitor and comply with the 15% limit on illiquid investments and for determining, periodically reviewing and complying with the HLIM requirement, as applicable.

There can be no assurance that the Program will achieve its objectives under all circumstances in the future. Please refer to the Fund's prospectus for more information regarding the Fund's exposure to liquidity risk and other risks to which it may be subject.

77

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Federal Tax Notice (unaudited)

For federal income tax purposes, the following information is furnished with respect to the distributions paid by the Fund during its taxable year ended September 30, 2020. For corporate shareholders, 26.86% of the dividends qualified for the dividends received deduction.

The Fund designated and paid approximately $1,055,000 as a long-term capital gain distribution. In addition, the Fund designated approximately $316,000 of its distributions paid as business interest income and approximately $9,000 of its distributions paid as qualified business income.

For federal income tax purposes, the following information is furnished with respect to the Fund's earnings for its taxable year ended September 30, 2020. When distributed, certain earnings may be subject to a maximum tax rate of 15% as provided for by the Jobs and Growth Tax Relief Reconciliation Act of 2003. The Fund designated up to a maximum of approximately $4,632,000 as taxable at this lower rate.

In January, the Fund provides tax information to shareholders for the preceding calendar year.

78

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Privacy Notice (unaudited)  April 2019

FACTS	WHAT DOES MSIM DO WITH YOUR PERSONAL INFORMATION?
Why?	Financial companies choose how they share your personal information. Federal law gives consumers the right to limit some but not all sharing. Federal law also requires us to tell you how we collect, share, and protect your personal information. Please read this notice carefully to understand what we do.
What?	The types of personal information we collect and share depend on the product or service you have with us. This information can include: n Social Security number and income n investment experience and risk tolerance n checking account number and wire transfer instructions
How?	All financial companies need to share customers' personal information to run their everyday business. In the section below, we list the reasons financial companies can share their customers' personal information; the reasons MSIM chooses to share; and whether you can limit this sharing.

Reasons we can share your personal information	Does MSIM share?	Can you limit this sharing?
For our everyday business purposes — such as to process your transactions, maintain your account(s), respond to court orders and legal investigations, or report to credit bureaus	Yes	No
For our marketing purposes — to offer our products and services to you	Yes	No
For joint marketing with other financial companies	No	We don't share
For our affiliates' everyday business purposes — information about your transactions and experiences	Yes	No
For our affiliates' everyday business purposes — information about your creditworthiness	No	We don't share
For our affiliates to market to you	No	We don't share
For non-affiliates to market to you	No	We don't share

Questions?Call toll-free (844) 312-6327 or email: imprivacyinquiries@morganstanley.com

79

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Privacy Notice (unaudited) (cont'd)  April 2019

Who we are

Who is providing this notice? Morgan Stanley Investment Management, Inc. and its affiliated registered investment advisers, registered broker-dealers, and registered and unregistered funds ("MSIM")

What we do

How does MSIM protect my personal information?	To protect your personal information from unauthorized access and use, we use security measures that comply with federal law. These measures include computer safeguards and secured files and buildings. We have policies governing the proper handling of customer information by personnel and requiring third parties that provide support to adhere to appropriate security standards with respect to such information.
How does MSIM collect my personal information?	We collect your personal information, for example, when you n open an account or make deposits or withdrawals from your account n buy securities from us or make a wire transfer n give us your contact information We also collect your personal information from others, such as credit bureaus, affiliates, or other companies.
Why can't I limit all sharing?	Federal law gives you the right to limit only n sharing for affiliates' everyday business purposes — information about your creditworthiness n affiliates from using your information to market to you n sharing for non-affiliates to market to you State laws and individual companies may give you additional rights to limit sharing. See below for more on your rights under state law.

Definitions

Affiliates	Companies related by common ownership or control. They can be financial and non-financial companies. n Our affiliates include companies with a Morgan Stanley name and financial companies such as Morgan Stanley Smith Barney LLC and Morgan Stanley & Co.
Non-affiliates	Companies not related by common ownership or control. They can be financial and non-financial companies. n MSIM does not share with non-affiliates so they can market to you.
Joint marketing	A formal agreement between non-affiliated financial companies that together market financial products or services to you. n MSIM doesn't jointly market

Other Important Information

Vermont: Except as permitted by law, we will not share personal information we collect about Vermont residents with Non-affiliates unless you provide us with your written consent to share such information.

California: Except as permitted by law, we will not share personal information we collect about California residents with Non-affiliates and we will limit sharing such personal information with our Affiliates to comply with California privacy laws that apply to us.

80

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited)

Independent Trustees:

Name, Address and Birth Year of Independent Trustee	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years and Other Relevant Professional Experience	Number of Funds in Fund Complex Overseen by Independent Trustee**		Other Directorships Held by Independent Trustee***
Frank L. Bowman c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1944	Trustee	Since August 2006	President, Strategic Decisions, LLC (consulting) (since February 2009); Director or Trustee of various Morgan Stanley Funds (since August 2006); Chairperson of the Compliance and Insurance Committee (since October 2015); formerly, Chairperson of the Insurance Sub-Committee of the Compliance and Insurance Committee (2007-2015); served as President and Chief Executive Officer of the Nuclear Energy Institute (policy organization) (February 2005-November 2008); retired as Admiral, U.S. Navy after serving over 38 years on active duty including 8 years as Director of the Naval Nuclear Propulsion Program in the Department of the Navy and the U.S. Department of Energy (1996-2004); served as Chief of Naval Personnel (July 1994-September 1996) and on the Joint Staff as Director of Political Military Affairs (June 1992-July 1994); knighted as Honorary Knight Commander of the Most Excellent Order of the British Empire; awarded the Officier de l'Orde National du Mérite by the French Government; elected to the National Academy of Engineering (2009).		86	Director of Naval and Nuclear Technologies LLP; Director Emeritus of the Armed Services YMCA; Member of the National Security Advisory Council of the Center for U.S. Global Engagement and a member of the CNA Military Advisory Board; Trustee of Fairhaven United Methodist Church; Member of the Board of Advisors of the Dolphin Scholarship Foundation; Director of other various non-profit organizations; Formerly, Director of BP p.l.c. (November 2010-May 2019).
Kathleen A. Dennis c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1953	Trustee	Since August 2006	President, Cedarwood Associates (mutual fund and investment management consulting) (since July 2006); Chairperson of the Liquidity and Alternatives Sub-Committee of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 2006); formerly, Senior Managing Director of Victory Capital Management (1993-2006).		86	Director of various non-profit organizations.
Nancy C. Everett c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1955	Trustee	Since January 2015	Chief Executive Officer, Virginia Commonwealth University Investment Company (since November 2015); Owner, OBIR, LLC (institutional investment management consulting) (since June 2014); formerly, Managing Director, BlackRock, Inc. (February 2011-December 2013); and Chief Executive Officer, General Motors Asset Management (a/k/a Promark Global Advisors, Inc.) (June 2005-May 2010).		87	Formerly, Member of Virginia Commonwealth University School of Business Foundation (2005-2016); Member of Virginia Commonwealth University Board of Visitors (2013-2015); Member of Committee on Directors for Emerging Markets Growth Fund, Inc. (2007-2010); Chairperson of Performance Equity Management, LLC (2006-2010); and Chairperson, GMAM Absolute Return Strategies Fund, LLC (2006-2010).

81

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Address and Birth Year of Independent Trustee	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years and Other Relevant Professional Experience	Number of Funds in Fund Complex Overseen by Independent Trustee**		Other Directorships Held by Independent Trustee***
Jakki L. Haussler c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1957	Trustee	Since January 2015	Chairman, Opus Capital Group (since January 1996); formerly, Chief Executive Officer, Opus Capital Group (1996-2019); Director, Capvest Venture Fund, LP (May 2000-December 2011); Partner, Adena Ventures, LP (July 1999-December 2010); Director, The Victory Funds (February 2005-July 2008).		87	Director of Service Corporation International and Member, Audit Committee and Investment Committee; Director of Cincinnati Bell Inc. and Member, Audit Committee and Governance and Nominating Committee; Director of Northern Kentucky University Foundation and Member, Investment Committee; Member of Chase College of Law Transactional Law Practice Center Board of Advisors; Director of Chase College of Law Board of Visitors; formerly, Member, University of Cincinnati Foundation Investment Committee; Member, Miami University Board of Visitors (2008-2011); Trustee of Victory Funds (2005-2008) and Chairman, Investment Committee (2007-2008); Member, Service Provider Committee (2005-2008) and Director of Best Transport (2006-2019).
Dr. Manuel H. Johnson c/o Johnson Smick International, Inc. 220 I Street, NE — Suite 200 Washington, D.C. 20002 Birth Year 1949	Trustee	Since July 1991	Senior Partner, Johnson Smick International, Inc. (consulting firm); Chairperson of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since July 1991); Co-Chairman and a founder of the Group of Seven Council (G7C) (international economic commission); formerly, Chairperson of the Audit Committee (July 1991-September 2006), Vice Chairman of the Board of Governors of the Federal Reserve System and Assistant Secretary of the U.S. Treasury.		86	Director of NVR, Inc. (home construction).
Joseph J. Kearns c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1942	Trustee	Since August 1994	Senior Adviser, Kearns & Associates LLC (investment consulting); Chairperson of the Audit Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 1994); Director, Rubicorn Investments (since February 2019); formerly, Deputy Chairperson of the Audit Committee (July 2003-September 2006) and Chairperson of the Audit Committee of various Morgan Stanley Funds (since August 1994); CFO of the J. Paul Getty Trust (1982-1999).		87	Prior to August 10, 2016, Director of Electro Rent Corporation (equipment leasing); Prior to December 31, 2013, Director of The Ford Family Foundation.

82

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Address and Birth Year of Independent Trustee	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years and Other Relevant Professional Experience	Number of Funds in Fund Complex Overseen by Independent Trustee**		Other Directorships Held by Independent Trustee***
Michael F. Klein c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1958	Trustee	Since August 2006	Managing Director, Aetos Alternatives Management, LP (since March 2000); Co-President, Aetos Alternatives Management, LP (since January 2004) and Co-Chief Executive Officer of Aetos Alternatives Management, LP (since August 2013); Chairperson of the Fixed Income Sub-Committee of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 2006); formerly, Managing Director, Morgan Stanley & Co. Inc. and Morgan Stanley Dean Witter Investment Management and President, various Morgan Stanley Funds (June 1998-March 2000); Principal, Morgan Stanley & Co. Inc. and Morgan Stanley Dean Witter Investment Management (August 1997-December 1999).		86	Director of certain investment funds managed or sponsored by Aetos Alternatives Management, LP; Director of Sanitized AG and Sanitized Marketing AG (specialty chemicals).
Patricia Maleski c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1960	Trustee	Since January 2017	Managing Director, JPMorgan Asset Management (2004-2016); Oversight and Control Head of Fiduciary and Conflicts of Interest Program (2015-2016); Chief Control Officer-Global Asset Management (2013-2015); President, JPMorgan Funds (2010-2013); Chief Administrative Officer (2004-2013); various other positions including Treasurer and Board Liaison (since 2001).		87	None.
W. Allen Reed c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1947	Chair of the Board and Trustee	Chair of the Boards since August 2020 and Trustee since August 2006	Chair of the Boards of various Morgan Stanley Funds (since August 2020); Chairperson of the Governance Committee; Chairperson of the Equity Sub-Committee of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 2006); formerly, Vice Chair of the Boards of various Morgan Stanley Funds (January 2020-August 2020); President and Chief Executive Officer of General Motors Asset Management; Chairman and Chief Executive Officer of the GM Trust Bank and Corporate Vice President of General Motors Corporation (August 1994-December 2005).		86	Formerly, Director of Legg Mason, Inc. (2006-2019); and Director of the Auburn University Foundation (2010-2015).

*  This is the earliest date the Trustee began serving the Morgan Stanley Funds. Each Trustee serves an indefinite term, until his or her successor is elected.

**  The Fund Complex includes (as of December 31, 2019) all open-end and closed-end funds (including all of their portfolios) advised by Morgan Stanley Investment Management Inc. (the "Adviser") and any funds that have an adviser that is an affiliated person of the Adviser (including, but not limited to, Morgan Stanley AIP GP LP).

***  This includes any directorships at public companies and registered investment companies held by the Trustee at any time during the past five years.

83

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited) (cont'd)

Executive Officers:

Name, Address and Birth Year of Executive Officer	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years
John H. Gernon 522 Fifth Avenue New York, NY 10036 Birth Year 1963	President and Principal Executive Officer	Since September 2013	President and Principal Executive Officer of the Equity and Fixed Income Funds and the Morgan Stanley AIP Funds (since September 2013) and the Liquidity Funds and various money market funds (since May 2014) in the Fund Complex; Managing Director of the Adviser; Head of Public Markets Product Development (since 2006).
Timothy J. Knierim 522 Fifth Avenue New York, NY 10036 Birth Year 1959	Chief Compliance Officer	Since December 2016	Managing Director of the Adviser and various entities affiliated with the Adviser; Chief Compliance Officer of various Morgan Stanley Funds and the Adviser (since December 2016) and Chief Compliance Officer of Morgan Stanley AIP GP LP (since 2014). Formerly, Managing Director and Deputy Chief Compliance Officer of the Adviser (2014-2016); and formerly, Chief Compliance Officer of Prudential Investment Management, Inc. (2007-2014).
Francis J. Smith 522 Fifth Avenue New York, NY 10036 Birth Year 1965	Treasurer and Principal Financial Officer	Treasurer since July 2003 and Principal Financial Officer since September 2002	Managing Director of the Adviser and various entities affiliated with the Adviser; Treasurer (since July 2003) and Principal Financial Officer of various Morgan Stanley Funds (since September 2002).
Mary E. Mullin 522 Fifth Avenue New York, NY 10036 Birth Year 1967	Secretary	Since June 1999	Managing Director of the Adviser; Secretary of various Morgan Stanley Funds (since June 1999).
Michael J. Key 522 Fifth Avenue New York, NY 10036 Birth Year 1979	Vice President	Since June 2017	Vice President of the Equity and Fixed Income Funds, Liquidity Funds, various money market funds and the Morgan Stanley AIP Funds in the Fund Complex (since June 2017); Executive Director of the Adviser; Head of Product Development for Equity and Fixed Income Funds (since August 2013).

*  This is the earliest date the officer began serving the Morgan Stanley Funds. Each officer serves a one-year term, until his or her successor is elected and qualifies.

84

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Adviser and Administrator

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

Sub-Adviser

Morgan Stanley Investment Management Limited
25 Cabot Square, Canary Wharf
London, E14 4QA, England

Distributor

Morgan Stanley Distribution, Inc.
522 Fifth Avenue
New York, New York 10036

Dividend Disbursing and Transfer Agent

DST Asset Manager Solutions, Inc.
2000 Crown Colony Drive
Quincy, Massachusetts 02169

Custodian

State Street Bank and Trust Company
One Lincoln Street
Boston, Massachusetts 02111

Legal Counsel

Dechert LLP
1095 Avenue of the Americas
New York, New York 10036

Counsel to the Independent Trustees

Perkins Coie LLP
1155 Avenue of the Americas,
22nd Floor
New York, New York 10036

Independent Registered Public Accounting Firm

Ernst & Young LLP
200 Clarendon Street
Boston, Massachusetts 02116

Reporting to Shareholders

Each Morgan Stanley fund provides a complete schedule of portfolio holdings in its Semi-Annual and the Annual Reports within 60 days of the end of the fund's second and fourth fiscal quarters. The Semi-Annual and Annual Reports are filed electronically with the Securities and Exchange Commission ("SEC") on Form N-CSRS and Form N-CSR, respectively. Morgan Stanley also delivers the Semi-Annual and Annual Reports to fund shareholders and makes these reports available on its public website, www.morganstanley.com/im/shareholderreports. Each Morgan Stanley non-money market fund also files a complete schedule of portfolio holdings with the SEC for the fund's first and third fiscal quarters as an attachment to Form N-PORT. Morgan Stanley does not deliver the reports for the first and third fiscal quarters to shareholders, nor are the reports posted to the Morgan Stanley public website. However, the holdings for each money market fund are posted to the Morgan Stanley public website. You may obtain the Form N-PORT filings (as well as the Form N-CSR and N-CSRS filings) by accessing the SEC's website, www.sec.gov. You can also request copies of these materials, upon payment of a duplicating fee, by electronic request at the SEC's email address (publicinfo@sec.gov).

Proxy Voting Policies and Procedures and Proxy Voting Record

You may obtain a copy of the Trust's Proxy Voting Policy and Procedures and information regarding how the Trust voted proxies relating to portfolio securities during the most recent twelve-month period ended June 30, without charge, upon request, by calling toll free 1 (800) 548-7786 or by visiting our website at www.morganstanley.com/im/shareholderreports. This information is also available on the SEC's website at www.sec.gov.

This report is authorized for distribution only when preceded or accompanied by a prospectus or summary prospectus of the applicable fund of Morgan Stanley Institutional Fund Trust., which describes in detail the fund's investment policies, risks, fees and expenses. Please read the prospectus carefully before you invest or send money. For additional information, including information regarding the investments comprising the Fund, please visit our website at www.morganstanley.com/im/shareholderreports or call toll free 1 (800) 548-7786.

85

Printed in U.S.A.
This Report has been prepared for shareholders and may be distributed to others only if preceded or accompanied by a current prospectus.

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

© 2020 Morgan Stanley. Morgan Stanley Distribution, Inc.

IFTGSANN
3300498 EXP 11.30.21

INVESTMENT MANAGEMENT

Morgan Stanley Institutional Fund Trust

High Yield Portfolio

Annual Report

September 30, 2020

Beginning on January 1, 2021, as permitted by regulations adopted by the Securities and Exchange Commission ("SEC"), paper copies of the Fund's Annual and Semi-Annual Reports to Shareholders ("Shareholder Reports") will no longer be sent by mail, unless you specifically request paper copies of the Shareholder Reports from the Fund or from your financial intermediary, such as a broker-dealer or a bank. Instead, the Shareholder Reports will be made available on the Fund's website, https://www.morganstanley.com/im/shareholderreports and you will be notified by mail each time a Shareholder Report is posted and provided with a website link to access the Shareholder Report. If you already elected to receive Shareholder Reports electronically, you will not be affected by this change and you need not take any action. You may elect to receive Shareholder Reports and other communications from the Fund electronically anytime by contacting your financial intermediary or, if you are a direct investor, please follow the instructions on the envelope.

Beginning on January 1, 2019, you may elect to receive all future Shareholder Reports in paper free of charge. If you invest through a financial intermediary, you can contact your financial intermediary to request that you continue to receive paper copies of your Shareholder Reports. If you invest directly with the Fund, please follow the instructions on the envelope to let the Fund know you wish to continue receiving paper copies of your Shareholder Reports. Your election to receive Shareholder Reports in paper will apply to all funds held in your account if you invest through your financial intermediary or all funds held with the fund complex if you invest directly with a fund.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Table of Contents

Shareholders' Letter	2
Expense Example	3
Investment Overview	4
Portfolio of Investments	7
Statement of Assets and Liabilities	15
Statement of Operations	17
Statements of Changes in Net Assets	18
Financial Highlights	20
Notes to Financial Statements	26
Report of Independent Registered Public Accounting Firm	34
Investment Advisory Agreement Approval	35
Liquidity Risk Management Program	37
Privacy Notice	38
Trustee and Officer Information	40

This report is authorized for distribution only when preceded or accompanied by a prospectus or summary prospectus of the applicable Fund of the Morgan Stanley Institutional Fund Trust. To receive a prospectus and/or statement of additional information ("SAI"), which contains more complete information such as investment objectives, charges, expenses, policies for voting proxies, risk considerations and describes in detail each of the Fund's investment policies to the prospective investor, please call toll free 1 (800) 548-7786. Please read the prospectuses carefully before you invest or send money.

Additionally, you can access information about the Fund, including performance, characteristics and investment team commentary, through Morgan Stanley Investment Management's website: www.morganstanley.com/im/shareholderreports.

Market forecasts provided in this report may not necessarily come to pass. There is no guarantee that any sectors mentioned will continue to perform as discussed herein or that securities in such sectors will be held by the Fund in the future. There is no assurance that a fund will achieve its investment objective. Funds are subject to market risk, which is the possibility that market values of securities owned by the Fund will decline and, therefore, the value of the Fund's shares may be less than what you paid for them. Accordingly, you can lose money investing in this Fund. Please see the prospectus for more complete information on investment risks.

1

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Shareholders' Letter (unaudited)

Dear Shareholders,

We are pleased to provide this Annual Report, in which you will learn how your investment in High Yield Portfolio (the "Fund") performed during the latest twelve-month period.

Morgan Stanley Investment Management is a client-centric, investor-led organization. Our global presence, intellectual capital, and breadth of products and services enable us to partner with investors to meet the evolving challenges of today's financial markets. We aim to deliver superior investment service and to empower our clients to make the informed decisions that help them reach their investment goals.

As always, we thank you for selecting Morgan Stanley Investment Management, and look forward to working with you in the months and years ahead.

Sincerely,

John H. Gernon
President and Principal Executive Officer

October 2020

2

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Expense Example (unaudited)

High Yield Portfolio

As a shareholder of the Fund, you may incur two types of costs: (1) transactional costs, including sales charge (loads) on purchase payments; and (2) ongoing costs, which may include advisory fees, administration fees, distribution and shareholder services fees; and other Fund expenses. This example is intended to help you understand your ongoing costs (in dollars) of investing in the Fund and to compare these costs with the ongoing costs of investing in other mutual funds.

This example is based on an investment of $1,000 invested at the beginning of the six-month period ended September 30, 2020 and held for the entire six-month period.

Actual Expenses

The table below provides information about actual account values and actual expenses. You may use the information in this table, together with the amount you invested, to estimate the expenses that you paid over the period. Simply divide your account value by $1,000 (for example, an $8,600 account value divided by $1,000 = 8.6), then multiply the result by the number in the table under the heading entitled "Actual Expenses Paid During Period" to estimate the expenses you paid on your account during this period.

Hypothetical Example for Comparison Purposes

The table below provides information about hypothetical account values and hypothetical expenses based on the Fund's actual expense ratio and an assumed rate of return of 5% per year before expenses, which is not the Fund's actual return. The hypothetical account values and expenses may not be used to estimate the actual ending account balance or expenses you paid for the period. You may use this information to compare the ongoing costs of investing in the Fund and other funds. To do so, compare this 5% hypothetical example with the 5% hypothetical examples that appear in the shareholder reports of the other funds.

Please note that the expenses shown in the table are meant to highlight your ongoing costs only and do not reflect any transactional costs, such as sales charges (loads, if applicable). Therefore, the information for each class in the table is useful in comparing ongoing costs only, and will not help you determine the relative total costs of owning different funds. In addition, if these transactional costs were included, your costs would have been higher.

	Beginning Account Value 4/1/20		Actual Ending Account Value 9/30/20		Hypothetical Ending Account Value		Actual Expenses Paid During Period*		Hypothetical Expenses Paid During Period*		Net Expense Ratio During Period**
High Yield Portfolio Class I	$	1,000.00	$	1,159.80	$	1,021.75	$	3.51	$	3.29		0.65	%
High Yield Portfolio Class A		1,000.00		1,156.40		1,020.00		5.39		5.05		1.00
High Yield Portfolio Class L		1,000.00		1,155.20		1,018.75		6.74		6.31		1.25
High Yield Portfolio Class C		1,000.00		1,153.00		1,016.30		9.37		8.77		1.74
High Yield Portfolio Class IS		1,000.00		1,160.00		1,021.90		3.35		3.13		0.62
High Yield Portfolio Class IR		1,000.00		1,160.00		1,021.90		3.35		3.13		0.62

*  Expenses are calculated using each Fund Class' annualized net expense ratio (as disclosed), multiplied by the average account value over the period and multiplied by 183/366 (to reflect the most recent one-half year period).

**  Annualized.

3

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Overview (unaudited)

High Yield Portfolio

The Fund seeks total return.

Performance

For the fiscal year ended September 30, 2020, the Fund's Class I shares had a total return based on net asset value and reinvestment of distributions per share of 0.15%, net of fees. The Fund's Class I shares underperformed against the Fund's benchmark, the Bloomberg Barclays U.S. Corporate High Yield Index (the "Index"), which returned 3.25%.

Factors Affecting Performance

•  The final quarter of 2019 provided a remarkable ending to a remarkable year. Credit markets enjoyed meaningful tightening in their spreads on the back of reduced U.S.-China trade tensions, improved economic data and the dovish stance from the Federal Reserve (Fed). Over the fourth quarter of 2019, the Index returned 2.61%, bringing 2019 full-year returns to 14.32%.ⁱ Yields tightened 46 basis points (bps) over the fourth quarter to end 2019 at 5.19%, while spreads tightened 45 bps to end the year at 357 bps.ⁱ

•  2020 began with a risk-off sentiment as escalation between the U.S. and Iran as well as the coronavirus outbreak in China weighed on investors. However, by the beginning of March 2020, this risk-off sentiment quickly became full-blown panic as the COVID-19 epidemic turned into a global pandemic, engulfing the rest of the world and leading to rapidly rising deaths and infections, lockdowns of populations and closing of economies. Extraordinary times were matched by extraordinary price action in the high yield market. At the end of the first quarter of 2020, spreads were 544 bps wider at 880 bps, and yields widened 425 bps to end March at 9.44%.ⁱ On March 23, 2020, at the peak of the sell-off, yields and spreads were 11.69% and 1123 bps, respectively.ⁱ What occurred in March 2020 was the fastest, most severe sell-off in high yield history. To put it in perspective, the spread widening that occurred over a six-month period in 2008 took 13 days in March 2020.ⁱ This March 2020 sell-off was then followed by a historic, top-three rebound that only trailed rallies seen in March 2001 and January 2009.ⁱ The Index gained 8.85% between March 23 and March 31, 2020.ⁱ

•  Unprecedented monetary relief measures, in addition to some better-than-expected economic

data, helped fuel a sharp rally that continued in the second quarter of 2020. The Index returned over 10% in the second quarter, the strongest quarterly returns in over a decade.ⁱ Spreads tightened 254 bps to end the second quarter at 626 bps, and yields fell 257 bps to 6.87%.ⁱ

•  The market continued to recover during the third quarter of 2020, though it ran out of steam in September amid a pickup in virus cases and uncertainty surrounding the prospect of another stimulus package ahead of the U.S. election. However, given the rebound we have seen in asset prices, a pause was to be expected. We view the September swoon as nothing more than constructive consolidation. The Index returned 4.60% in the third quarter of 2020, bringing year-to-date returns to 0.62% as of September 30, 2020.ⁱ Spreads tightened 109 bps to end the third quarter at 517 bps, and yields fell 110 bps to 5.77%.ⁱ Spreads and yields are now just 181 bps and 58 bps wider on a year-to-date basis as of September 30, 2020, and 583 bps and 592 bps tighter since March 23, 2020.ⁱ

•  While volatility with regard to policy, politics and the pandemic have increased, we believe fundamentals continue to support an economic recovery, albeit slower than what we enjoyed in the third quarter. Employment has continued to rebound, global trade and manufacturing have remained in strong recovery mode, and consumer spending in particular has remained robust, with retail sales moving above pre-COVID-19 levels in many developed countries.

•  While the Fund had been outperforming the Index though February 2020 over nearly all time periods, the month of March proved to be a difficult one for both the markets and the Fund. In March 2020 alone, the Fund returned -15.15% (net of fees), underperforming the benchmark return of -11.46%.

•  Our sector positioning was a major factor going into the downturn and subsequent underperformance. The portfolio was positioned to be overweight the consumer cyclicals sectors, as the strong U.S. consumer remained the linchpin of the U.S. economy. However, given the rapid spread of COVID-19, many of these sectors saw an almost

ⁱ  Source: Bloomberg Barclays.

4

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Overview (unaudited) (cont'd)

High Yield Portfolio

immediate cessation of revenues because of various travel restrictions and stay-at-home ordinances issued globally. As a result, overweight positioning to consumer cyclicals detracted over the 12-month period. The Fund's broad underweight to communications and technology also detracted over the period as both of these sectors have been relatively insulated from the effects of COVID-19 and, in some circumstances, actually benefited from increased demand. Work-from-home requirements drove demand in various tech sectors (e.g., increased software demand for virtualization, end-point security, recovery and backups, and cloud access), and with most of the country ordered to stay at home, there has been a strong demand for media/telecom/wireless and wirelines.

•  This relative weakness was partially offset by an underweight to airlines as well as overweights to defensive sectors such as packaging and food & beverage, which were additive.

•  The Fund's underweight positioning to energy, particularly some "fallen angel" credits (bonds that were downgraded from investment grade to high yield), detracted over the period as well, as these credits rallied on the back of an improving commodity backdrop.

•  From a ratings perspective, the Fund's underweight to BB-rated bonds detracted from performance as higher-quality bonds outperformed over the period. An off-benchmark allocation to bank loans also detracted from returns.

Management Strategies

•  We have added some higher-quality fallen angels and selectively added larger ETF-eligible names that we believe may benefit (whether directly or indirectly) from the Fed's corporate credit facilities.

•  We have been actively participating in the new issue calendar as the primary market continues to present opportunities — new issue premiums have been high and new bonds have generally traded well. We continue to sell credits that we think are at near-term default risk and have sold some BB-rated securities trading at very tight levels. While we remain underweight the energy sector, we continue increase high-grade exposure within this sector, and have added producers in high-quality basins with low leverage that we believe can make it through the current environment.

•  We expect to see a meaningful increase in overall defaults in the coming year due to a weaker economy stemming from the outbreak, as well as stress in the energy sector. However, with a significant reduction in default activity over the last two months, and a far quicker recovery from the COVID-19 shock than initially anticipated, we expect default rates to be a more muted 6% to 8%, as opposed to the 10% to 12% initially forecast. We still expect all to be heavily concentrated in energy and coronavirus-impacted sectors, so getting sector positioning right will be critical for performance over the coming months.

•  Going into the final quarter of 2020, we continue to expect monetary policy to remain accommodative and risk assets to be well supported across developed markets. On the other hand, our relatively constructive view is tempered by less compelling valuations and some setbacks in the fight against the pandemic, as evidenced in increasing case counts in Europe and the U.S. While we remain cautiously optimistic that developments could lead to even tighter spreads by year-end or in 2021, we expect some near-term volatility as we approach the November U.S. election.

*  Minimum Investment

**  Commenced operations on February 7, 2012.

In accordance with SEC regulations, the Fund's performance shown assumes that all recurring fees (including management fees) were deducted and all dividends and distributions were reinvested. The performance of Class A, Class L, Class C, Class IS and Class IR shares will vary from the performance of Class I shares based upon their different inception dates and will be negatively impacted by additional fees assessed to those classes (where applicable).

5

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Overview (unaudited) (cont'd)

High Yield Portfolio

Performance Compared to the Bloomberg Barclays U.S. Corporate High Yield Index⁽¹⁾ and the Lipper High Current Yield Bond Funds Index⁽²⁾

	Period Ended September 30, 2020 Total Returns(3)
				Average Annual
	One Year			Five Years			Ten Years		Since Inception(8)
Fund — Class I Shares w/o sales charges(4)		0.15	%		5.54	%		—		6.81	%
Fund — Class A Shares w/o sales charges(4)		-0.22			5.14			—		6.44
Fund — Class A Shares with maximum 3.25% sales charges(4)		-3.48			4.45			—		6.03
Fund — Class L Shares w/o sales charges(4)		-0.46			4.88			—		6.18
Fund — Class C Shares w/o sales charges(6)		-0.93			4.40			—		3.32
Fund — Class C Shares with maximum 1.00% deferred sales charges(6)		-1.87			4.40			—		3.32
Fund — Class IS Shares w/o sales charges(5)		0.18			5.57			—		4.04
Fund — Class IR Shares w/o sales charges(7)		0.18			—			—		2.96
Bloomberg Barclays U.S. Corporate High Yield Index		3.25			6.79			—		6.06
Lipper High Current Yield Bond Funds Index		1.19			5.54			—		5.27

Performance data quoted represents past performance, which is no guarantee of future results, and current performance may be lower or higher than the figures shown. Performance assumes that all dividends and distributions, if any, were reinvested. For the most recent month-end performance figures, please visit www.morganstanley.com/im/shareholderreports. Investment returns and principal value will fluctuate so that Fund shares, when redeemed, may be worth more or less than their original cost. Total returns do not reflect the deduction of taxes that a shareholder would pay on Fund distributions or the redemption of Fund shares. Performance of share classes will vary due to differences in sales charges and expenses.

⁽¹⁾  The Bloomberg Barclays U.S. Corporate High Yield Index measures the market of USD-denominated, non-investment grade, fixed-rate, taxable corporate bonds. Securities are classified as high yield if the middle rating of Moody's, Fitch, and S&P is Ba1/BB+/BB+ or below. The index excludes emerging market debt. The Index is unmanaged and its returns do not include any sales charges or fees. Such costs would lower performance. It is not possible to invest directly in an index.

⁽²⁾  The Lipper High Current Yield Bond Funds Index is an equally weighted performance index of the largest qualifying funds (based on net assets) in the Lipper High Current Yield Bond Funds classification. The Index, which is adjusted for capital gains distributions and income dividends, is unmanaged and should not be considered an investment. There are currently 30 funds represented in this Index. As of the date of this report, the Fund was in the Lipper High Current Yield Bond Funds classification.

⁽³⁾  Total returns for the Fund reflect expenses waived and/or reimbursed, if applicable, by the Adviser. Without such waivers and/or reimbursements, total returns would have been lower.

⁽⁴⁾  Commenced operations on February 7, 2012.

⁽⁵⁾  Commenced offering on March 28, 2014.

⁽⁶⁾  Commenced offering on April 30, 2015.

⁽⁷⁾  Commenced offering on June 15, 2018.

⁽⁸⁾  For comparative purposes, average annual since inception returns listed for the Indexes refer to the inception date of Class I of the Fund, not the inception of the Indexes.

6

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments

High Yield Portfolio

	Face Amount (000)		Value (000)
Fixed Income Securities (97.8%)
Corporate Bonds (94.6%)
Basic Materials (5.5%)
Alcoa Nederland Holding BV
5.50%, 12/15/27 (a)	$	500	$	522
Avient Corp.
5.75%, 5/15/25 (a)		500		531
Axalta Coating Systems LLC/Axalta Coating Systems Dutch Holding B BV
4.75%, 6/15/27 (a)		225		230
Chemours Co. (The)
6.63%, 5/15/23		750		761
Eldorado Gold Corp.
9.50%, 6/1/24 (a)		789		841
First Quantum Minerals Ltd.,
6.88%, 10/15/27 (a)(b)		250		241
7.50%, 4/1/25 (a)		500		495
Hudbay Minerals, Inc.,
6.13%, 4/1/29 (a)		325		323
7.63%, 1/15/25 (a)		250		255
IAMGOLD Corp.
5.75%, 10/15/28 (a)		550		535
Innophos Holdings, Inc.
9.38%, 2/15/28 (a)		1,000		1,067
International Wire Group, Inc.
10.75%, 8/1/21 (a)		650		579
Kaiser Aluminum Corp.,
4.63%, 3/1/28 (a)		400		374
6.50%, 5/1/25 (a)		300		310
Minerals Technologies, Inc.
5.00%, 7/1/28 (a)		500		519
Novelis Corp.
4.75%, 1/30/30 (a)		600		590
Olin Corp.
9.50%, 6/1/25 (a)		425		496
PQ Corp.
5.75%, 12/15/25 (a)		575		594
Schweitzer-Mauduit International, Inc.
6.88%, 10/1/26 (a)		850		900
				10,163
Communications (12.3%)
Altice Financing SA
5.00%, 1/15/28 (a)		550		535
Altice France SA,
5.13%, 1/15/29 (a)		250		249
7.38%, 5/1/26 (a)		500		524
Avaya, Inc.
6.13%, 9/15/28 (a)		500		512
Block Communications, Inc.
4.88%, 3/1/28 (a)		800		818
C&W Senior Financing DAC
6.88%, 9/15/27 (a)		500		521

	Face Amount (000)		Value (000)
CCO Holdings LLC/CCO Holdings Capital Corp.
5.00%, 2/1/28 (a)	$	800	$	841
CenturyLink, Inc.
4.00%, 2/15/27 (a)		500		509
Clear Channel Worldwide Holdings, Inc.,
5.13%, 8/15/27 (a)		250		240
9.25%, 2/15/24		851		827
CSC Holdings LLC
5.75%, 1/15/30 (a)		985		1,048
Diamond Sports Group LLC/Diamond Sports Finance Co.
6.63%, 8/15/27 (a)		650		339
DISH DBS Corp.
7.75%, 7/1/26		500		550
Entercom Media Corp.
6.50%, 5/1/27 (a)		900		786
EW Scripps Co. (The)
5.13%, 5/15/25 (a)		1,000		980
GCI LLC
4.75%, 10/15/28 (a)(b)		300		304
Gray Television, Inc.
5.88%, 7/15/26 (a)		900		935
iHeartCommunications, Inc.
5.25%, 8/15/27 (a)		750		732
Lamar Media Corp.
4.00%, 2/15/30 (a)		250		250
LCPR Senior Secured Financing DAC
6.75%, 10/15/27 (a)		1,050		1,099
Level 3 Financing, Inc.
4.63%, 9/15/27 (a)		500		515
MDC Partners, Inc.
6.50%, 5/1/24 (a)		1,039		950
Midcontinent Communications/Midcontinent Finance Corp.
5.38%, 8/15/27 (a)		1,000		1,031
Nexstar Broadcasting, Inc.
5.63%, 7/15/27 (a)		550		579
Outfront Media Capital LLC/Outfront Media Capital Corp.
4.63%, 3/15/30 (a)		750		721
Radiate Holdco LLC / Radiate Finance, Inc.
6.50%, 9/15/28 (a)		750		771
Sable International Finance Ltd.
5.75%, 9/7/27 (a)		500		523
Sirius XM Radio, Inc.
5.00%, 8/1/27 (a)		500		522
Switch Ltd.
3.75%, 9/15/28 (a)		300		304
TEGNA, Inc.,
4.63%, 3/15/28 (a)		450		441
5.00%, 9/15/29 (a)		300		297
TripAdvisor, Inc.
7.00%, 7/15/25 (a)		175		183

The accompanying notes are an integral part of the financial statements.
7

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

High Yield Portfolio

	Face Amount (000)		Value (000)
Communications (cont'd)
Univision Communications, Inc.,
6.63%, 6/1/27 (a)	$	425	$	416
9.50%, 5/1/25 (a)		850		914
Virgin Media Finance PLC
5.00%, 7/15/30 (a)		900		897
Ziggo Bond Co. BV
5.13%, 2/28/30 (a)		525		532
Ziggo BV
4.88%, 1/15/30 (a)		350		363
				22,558
Consumer, Cyclical (24.2%)
AAG FH LP/AAG FH Finco, Inc.
9.75%, 7/15/24 (a)		550		521
Adient US LLC
9.00%, 4/15/25 (a)		275		304
American Axle & Manufacturing, Inc.
6.88%, 7/1/28		650		632
American Builders & Contractors Supply Co., Inc.
5.88%, 5/15/26 (a)		350		364
Aramark Services, Inc.,
4.75%, 6/1/26		250		253
6.38%, 5/1/25 (a)		600		626
Asbury Automotive Group, Inc.
4.75%, 3/1/30 (a)		250		252
Ashton Woods USA LLC/Ashton Woods Finance Co.
6.63%, 1/15/28 (a)		725		730
Aston Martin Capital Holdings Ltd.
6.50%, 4/15/22 (a)		650		585
At Home Holding III, Inc.
8.75%, 9/1/25 (a)		750		785
Banijay Entertainment SASU
5.38%, 3/1/25 (a)		825		833
Beacon Roofing Supply, Inc.
4.88%, 11/1/25 (a)		500		491
Beazer Homes USA, Inc.
5.88%, 10/15/27		750		761
Boyd Gaming Corp.,
4.75%, 12/1/27		200		197
6.00%, 8/15/26		750		776
Boyne USA, Inc.
7.25%, 5/1/25 (a)		830		874
Burlington Coat Factory Warehouse Corp.
6.25%, 4/15/25 (a)		750		791
Carvana Co.
5.88%, 10/1/28 (a)(b)		600		594
CCM Merger, Inc.
6.00%, 3/15/22 (a)		750		742
CD&R Smokey Buyer, Inc.
6.75%, 7/15/25 (a)		750		792
Century Communities, Inc.,
5.88%, 7/15/25		500		522
6.75%, 6/1/27		300		317

	Face Amount (000)		Value (000)
Core & Main Holdings LP
8.63% CASH, 9.38% PIK, 9/15/24 (a)(c)	$	350	$	354
Dana, Inc.
5.38%, 11/15/27		500		513
Dealer Tire LLC / DT Issuer LLC
8.00%, 2/1/28 (a)		525		537
Delta Air Lines, Inc./SkyMiles IP Ltd.
4.75%, 10/20/28 (a)		850		884
Downstream Development Authority of the Quapaw Tribe of Oklahoma
10.50%, 2/15/23 (a)		1,268		1,171
Eagle Intermediate Global Holding BV/ Ruyi US Finance LLC
7.50%, 5/1/25 (a)		425		300
FelCor Lodging LP
6.00%, 6/1/25		500		492
Ferrellgas LP/Ferrellgas Finance Corp.
10.00%, 4/15/25 (a)		550		597
Ford Motor Co.,
8.50%, 4/21/23		575		628
9.00%, 4/22/25		750		861
Ford Motor Credit Co. LLC
4.13%, 8/17/27		250		244
Forestar Group, Inc.
5.00%, 3/1/28 (a)		500		506
G-III Apparel Group Ltd.
7.88%, 8/15/25 (a)		400		404
Golden Nugget, Inc.
8.75%, 10/1/25 (a)		600		474
Hanesbrands, Inc.
4.88%, 5/15/26 (a)		250		267
Installed Building Products, Inc.
5.75%, 2/1/28 (a)		250		264
International Game Technology PLC
5.25%, 1/15/29 (a)		375		380
IRB Holding Corp.
7.00%, 6/15/25 (a)		500		534
JB Poindexter & Co., Inc.
7.13%, 4/15/26 (a)		700		745
Ken Garff Automotive LLC
4.88%, 9/15/28 (a)		275		271
LGI Homes, Inc.
6.88%, 7/15/26 (a)		500		524
Lithia Motors, Inc.
4.63%, 12/15/27 (a)		600		621
Macy's, Inc.
8.38%, 6/15/25 (a)		750		776
Marriott Ownership Resorts, Inc.
6.13%, 9/15/25 (a)		450		465
Mattamy Group Corp.
5.25%, 12/15/27 (a)		500		515
Mclaren Finance PLC
5.75%, 8/1/22 (a)		550		499

The accompanying notes are an integral part of the financial statements.
8

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

High Yield Portfolio

	Face Amount (000)		Value (000)
Consumer, Cyclical (cont'd)
Meritor, Inc.,
6.25%, 2/15/24	$	350	$	358
6.25%, 6/1/25 (a)		250		262
MGM Resorts International,
5.50%, 4/15/27		327		342
6.75%, 5/1/25		500		525
Mileage Plus Holdings LLC/Mileage Plus Intellectual Property Assets Ltd.
6.50%, 6/20/27 (a)		750		783
Nathan's Famous, Inc.
6.63%, 11/1/25 (a)		1,000		1,020
National CineMedia LLC
5.75%, 8/15/26		500		342
Navistar International Corp.
6.63%, 11/1/25 (a)		750		768
New Home Co., Inc. (The)
7.25%, 4/1/22		750		747
Panther BF Aggregator 2 LP/Panther Finance Co., Inc.
8.50%, 5/15/27 (a)		465		481
Performance Food Group, Inc.,
5.50%, 10/15/27 (a)		710		733
6.88%, 5/1/25 (a)		500		535
Picasso Finance Sub, Inc.
6.13%, 6/15/25 (a)		625		674
Powdr Corp.
6.00%, 8/1/25 (a)		750		770
Rite Aid Corp.,
7.50%, 7/1/25 (a)		275		271
8.00%, 11/15/26 (a)		380		381
Sally Holdings LLC/Sally Capital, Inc.
5.63%, 12/1/25		500		508
Scientific Games International, Inc.,
7.00%, 5/15/28 (a)		225		226
8.25%, 3/15/26 (a)		500		523
Speedway Motorsports LLC/Speedway Funding II, Inc.
4.88%, 11/1/27 (a)		500		481
Spirit Loyalty Cayman Ltd./Spirit IP Cayman Ltd.
8.00%, 9/20/25 (a)		500		530
Station Casinos LLC
4.50%, 2/15/28 (a)		550		507
Sugarhouse HSP Gaming Prop Mezz LP/ Sugarhouse HSP Gaming Finance Corp.
5.88%, 5/15/25 (a)		810		793
Taylor Morrison Communities, Inc.
5.88%, 6/15/27 (a)		450		496
Tempur Sealy International, Inc.
5.50%, 6/15/26		425		442
Titan International, Inc.
6.50%, 11/30/23		900		676

	Face Amount (000)		Value (000)
Truck Hero, Inc.
8.50%, 4/21/24 (a)	$	1,100	$	1,170
Vail Resorts, Inc.
6.25%, 5/15/25 (a)		575		611
Winnebago Industries, Inc.
6.25%, 7/15/28 (a)		550		581
Wolverine World Wide, Inc.,
5.00%, 9/1/26 (a)		500		503
6.38%, 5/15/25 (a)		300		318
Wyndham Destinations, Inc.
4.63%, 3/1/30 (a)		500		483
				44,408
Consumer, Non-Cyclical (12.2%)
Acadia Healthcare Co., Inc.
5.50%, 7/1/28 (a)		600		618
AdaptHealth LLC
6.13%, 8/1/28 (a)		350		363
Ahern Rentals, Inc.
7.38%, 5/15/23 (a)		925		494
Albertsons Cos., Inc./Safeway, Inc./ New Albertson's, Inc./Albertson's LLC
5.88%, 2/15/28 (a)		250		267
Bausch Health Cos, Inc.,
6.13%, 4/15/25 (a)		100		102
9.00%, 12/15/25 (a)		550		600
Beverages & More, Inc.
11.50%, 6/15/22 (a)		900		759
Catalent Pharma Solutions, Inc.
5.00%, 7/15/27 (a)		500		521
Central Garden & Pet Co.
5.13%, 2/1/28		450		474
Chobani LLC/Chobani Finance Corp., Inc.
7.50%, 4/15/25 (a)		950		985
Edgewell Personal Care Co.
5.50%, 6/1/28 (a)		500		527
Emergent BioSolutions, Inc.
3.88%, 8/15/28 (a)		275		277
Endo Dac/Endo Finance LLC/Endo Finco, Inc.
6.00%, 7/15/23 (a)		778		617
FAGE International SA/FAGE USA Dairy Industry, Inc.
5.63%, 8/15/26 (a)		500		482
Garda World Security Corp.
9.50%, 11/1/27 (a)		900		947
Great Lakes Dredge & Dock Corp.
8.00%, 5/15/22		650		669
H-Food Holdings LLC/Hearthside Finance Co., Inc.
8.50%, 6/1/26 (a)		1,000		981
Hadrian Merger Sub, Inc.
8.50%, 5/1/26 (a)		350		349
Harsco Corp.
5.75%, 7/31/27 (a)		700		710
Jaguar Holding Co. II/PPD Development LP
5.00%, 6/15/28 (a)		300		313

The accompanying notes are an integral part of the financial statements.
9

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

High Yield Portfolio

	Face Amount (000)		Value (000)
Consumer, Non-Cyclical (cont'd)
Lamb Weston Holdings, Inc.
4.88%, 11/1/26 (a)	$	500	$	522
Michael Baker International LLC
8.75%, 3/1/23 (a)		800		800
MPH Acquisition Holdings LLC
7.13%, 6/1/24 (a)		750		771
Nielsen Finance LLC/Nielsen Finance Co.
5.63%, 10/1/28 (a)		625		648
Polaris Intermediate Corp.
8.50% CASH, 9.25% PIK, 12/1/22 (a)(c)		650		662
Post Holdings, Inc.
5.50%, 12/15/29 (a)		150		161
Select Medical Corp.
6.25%, 8/15/26 (a)		650		677
Service Corp. International
5.13%, 6/1/29		250		277
Simmons Foods, Inc.
5.75%, 11/1/24 (a)		600		602
Sotheby's
7.38%, 10/15/27 (a)		450		451
Spectrum Brands, Inc.
5.00%, 10/1/29 (a)		500		520
Surgery Center Holdings, Inc.,
6.75%, 7/1/25 (a)		650		649
10.00%, 4/15/27 (a)		700		747
Teleflex, Inc.
4.88%, 6/1/26		350		363
Tenet Healthcare Corp.,
6.13%, 10/1/28 (a)		250		244
7.00%, 8/1/25		600		619
Teva Pharmaceutical Finance Netherlands III BV
3.15%, 10/1/26		540		477
TMS International Holding Corp.
7.25%, 8/15/25 (a)		1,000		939
TreeHouse Foods, Inc.
4.00%, 9/1/28		225		228
United Rentals North America, Inc.
4.88%, 1/15/28		250		263
US Foods, Inc.
6.25%, 4/15/25 (a)		686		727
				22,402
Diversified (1.0%)
PetSmart, Inc.
7.13%, 3/15/23 (a)		800		808
Trident TPI Holdings, Inc.
6.63%, 11/1/25 (a)		1,000		989
				1,797
Energy (10.6%)
American Midstream Partners LP/American Midstream Finance Corp.
9.50%, 12/15/21 (a)		1,000		996

	Face Amount (000)		Value (000)
Archrock Partners LP/Archrock Partners Finance Corp.
6.88%, 4/1/27 (a)	$	300	$	288
Baytex Energy Corp.
5.63%, 6/1/24 (a)		1,000		569
Blue Racer Midstream LLC/Blue Racer Finance Corp.
6.63%, 7/15/26 (a)		850		751
CrownRock LP/CrownRock Finance, Inc.
5.63%, 10/15/25 (a)		750		709
Endeavor Energy Resources LP/EER Finance, Inc.,
5.75%, 1/30/28 (a)		750		755
6.63%, 7/15/25 (a)		250		257
Energy Ventures Gom LLC/EnVen Finance Corp.
11.00%, 2/15/23 (a)		1,200		904
Global Partners LP/GLP Finance Corp.
7.00%, 8/1/27		840		859
Jagged Peak Energy LLC
5.88%, 5/1/26		750		748
Lonestar Resources America, Inc.
11.25%, 1/1/23 (a)(d)(e)		1,115		201
Magnolia Oil & Gas Operating LLC/ Magnolia Oil & Gas Finance Corp.
6.00%, 8/1/26 (a)		700		693
Martin Midstream Partners LP/ Martin Midstream Finance Corp.,
10.00%, 2/29/24 (a)		218		227
11.50%, 2/28/25 (a)		992		903
Matador Resources Co.
5.88%, 9/15/26		800		670
Murphy Oil Corp.,
5.75%, 8/15/25		800		700
5.88%, 12/1/27		200		171
Murphy Oil USA, Inc.
5.63%, 5/1/27		800		853
NuStar Logistics LP
6.38%, 10/1/30		185		192
Occidental Petroleum Corp.,
2.90%, 8/15/24		875		744
6.95%, 7/1/24		875		849
Oceaneering International, Inc.
6.00%, 2/1/28		775		487
Parkland Fuel Corp.
5.88%, 7/15/27 (a)		250		263
Parsley Energy LLC/Parsley Finance Corp.
5.38%, 1/15/25 (a)		500		500
PBF Holding Co., LLC/PBF Finance Corp.
6.00%, 2/15/28 (a)		750		505
Rockies Express Pipeline LLC
3.60%, 5/15/25 (a)		500		491
Seven Generations Energy Ltd.
5.38%, 9/30/25 (a)		700		665

The accompanying notes are an integral part of the financial statements.
10

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

High Yield Portfolio

	Face Amount (000)		Value (000)
Energy (cont'd)
Tallgrass Energy Partners LP/ Tallgrass Energy Finance Corp.
7.50%, 10/1/25 (a)	$	200	$	201
Targa Resources Partners LP/Targa Resources Partners Finance Corp.
5.50%, 3/1/30 (a)		500		501
TransMontaigne Partners LP/TLP Finance Corp.
6.13%, 2/15/26		350		364
Vermilion Energy, Inc.
5.63%, 3/15/25 (a)		750		625
Viper Energy Partners LP
5.38%, 11/1/27 (a)		830		819
WPX Energy, Inc.,
4.50%, 1/15/30		300		296
5.25%, 10/15/27		700		712
				19,468
Finance (7.8%)
AHP Health Partners, Inc.
9.75%, 7/15/26 (a)		940		1,011
Alliant Holdings Intermediate LLC/ Alliant Holdings Co-Issuer
6.75%, 10/15/27 (a)		650		683
Compass Group Diversified Holdings LLC
8.00%, 5/1/26 (a)		700		737
CTR Partnership LP/CareTrust Capital Corp.
5.25%, 6/1/25		608		625
Cushman & Wakefield US Borrower LLC
6.75%, 5/15/28 (a)		400		417
Fly Leasing Ltd.
5.25%, 10/15/24		675		558
Freedom Mortgage Corp.
8.25%, 4/15/25 (a)		500		511
GTCR AP Finance, Inc.
8.00%, 5/15/27 (a)		600		635
HUB International Ltd.
7.00%, 5/1/26 (a)		582		604
Hunt Cos., Inc.
6.25%, 2/15/26 (a)		661		636
Icahn Enterprises LP/Icahn Enterprises Finance Corp.
5.25%, 5/15/27		250		261
INTL FCStone, Inc.
8.63%, 6/15/25 (a)		649		702
Iron Mountain, Inc.
5.25%, 7/15/30 (a)		300		313
iStar, Inc.
4.25%, 8/1/25		250		234
Kennedy-Wilson, Inc.
5.88%, 4/1/24		500		498
Lions Gate Capital Holdings LLC,
5.88%, 11/1/24 (a)		250		247
6.38%, 2/1/24 (a)		450		447

	Face Amount (000)		Value (000)
MGIC Investment Corp.
5.25%, 8/15/28	$	300	$	310
MGM Growth Properties Operating Partnership LP/MGP Finance Co-Issuer, Inc.
5.75%, 2/1/27		325		351
MGM Growth Properties Operating Partnership LP/ MGP Finance Co-Issuer, Inc.
4.63%, 6/15/25 (a)		150		153
MPT Operating Partnership LP/MPT Finance Corp.
4.63%, 8/1/29		500		521
NMI Holdings, Inc.
7.38%, 6/1/25 (a)		500		535
Oxford Finance LLC/Oxford Finance Co-Issuer II, Inc.
6.38%, 12/15/22 (a)		750		734
PennyMac Financial Services, Inc.
5.38%, 10/15/25 (a)		375		380
Provident Funding Associates LP/PFG Finance Corp.
6.38%, 6/15/25 (a)		462		449
Radian Group, Inc.
6.63%, 3/15/25		450		476
RHP Hotel Properties LP/RHP Finance Corp.
4.75%, 10/15/27		250		231
SBA Communications Corp.
3.88%, 2/15/27 (a)		425		432
Vertical US Newco, Inc.
5.25%, 7/15/27 (a)		550		573
				14,264
Health Care (0.1%)
Encompass Health Corp.
4.63%, 4/1/31		150		150
Industrials (16.8%)
American Woodmark Corp.
4.88%, 3/15/26 (a)		250		254
Apex Tool Group LLC/BC Mountain Finance, Inc.
9.00%, 2/15/23 (a)		900		835
Bombardier, Inc.
6.13%, 1/15/23 (a)		600		514
Brand Industrial Services, Inc.
8.50%, 7/15/25 (a)		1,000		947
Builders FirstSource, Inc.
5.00%, 3/1/30 (a)		500		518
Cargo Aircraft Management, Inc.
4.75%, 2/1/28 (a)		500		506
Cleaver-Brooks, Inc.
7.88%, 3/1/23 (a)		850		823
Core & Main LP
6.13%, 8/15/25 (a)		600		609
Cornerstone Building Brands, Inc.
8.00%, 4/15/26 (a)		650		684
Cornerstone Building Brands, Inc.
6.13%, 1/15/29 (a)		275		279
EnerSys
4.38%, 12/15/27 (a)		350		358

The accompanying notes are an integral part of the financial statements.
11

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

High Yield Portfolio

	Face Amount (000)		Value (000)
Industrials (cont'd)
EnPro Industries, Inc.
5.75%, 10/15/26	$	650	$	688
Flex Acquisition Co., Inc.
6.88%, 1/15/25 (a)		600		602
FXI Holdings, Inc.
7.88%, 11/1/24 (a)		688		655
GPC Merger Sub, Inc.
7.13%, 8/15/28 (a)		550		574
Greif, Inc.
6.50%, 3/1/27 (a)		175		182
Griffon Corp.
5.75%, 3/1/28		875		915
Grinding Media, Inc./Moly-Cop AltaSteel Ltd.
7.38%, 12/15/23 (a)		925		939
Ingram Micro, Inc.
5.45%, 12/15/24		750		803
Intelligent Packaging Ltd. Finco, Inc./Intelligent Packaging Ltd. Co-Issuer LLC
6.00%, 9/15/28 (a)		425		432
Intertape Polymer Group, Inc.
7.00%, 10/15/26 (a)		1,075		1,133
JPW Industries Holding Corp.
9.00%, 10/1/24 (a)		1,050		993
KBR, Inc.
4.75%, 9/30/28 (a)		330		332
Kenan Advantage Group, Inc. (The)
7.88%, 7/31/23 (a)		1,000		974
Koppers, Inc.
6.00%, 2/15/25 (a)		750		762
Kratos Defense & Security Solutions, Inc.
6.50%, 11/30/25 (a)		750		786
Manitowoc Co., Inc. (The)
9.00%, 4/1/26 (a)		575		595
Mauser Packaging Solutions Holding Co.
7.25%, 4/15/25 (a)		1,000		943
Moog, Inc.
4.25%, 12/15/27 (a)		500		512
New Enterprise Stone & Lime Co., Inc.,
6.25%, 3/15/26 (a)		575		593
9.75%, 7/15/28 (a)		500		543
Owens-Brockway Glass Container, Inc.
6.63%, 5/13/27 (a)		500		543
PGT Escrow Issuer, Inc.
6.75%, 8/1/26 (a)		750		801
Plastipak Holdings, Inc.
6.25%, 10/15/25 (a)		750		751
Standard Industries, Inc.
5.00%, 2/15/27 (a)		500		521
Stevens Holding Co., Inc.
6.13%, 10/1/26 (a)		350		376

	Face Amount (000)		Value (000)
Summit Materials LLC/Summit Materials Finance Corp.
5.25%, 1/15/29 (a)	$	500	$	522
TopBuild Corp.
5.63%, 5/1/26 (a)		500		518
TransDigm, Inc.
5.50%, 11/15/27		750		722
TriMas Corp.
4.88%, 10/15/25 (a)		350		355
Triumph Group, Inc.,
6.25%, 9/15/24 (a)		500		427
8.88%, 6/1/24 (a)		275		294
Trivium Packaging Finance BV
8.50%, 8/15/27 (a)		550		594
TTM Technologies, Inc.
5.63%, 10/1/25 (a)		1,013		1,037
Tutor Perini Corp.
6.88%, 5/1/25 (a)		750		691
US Concrete, Inc.,
5.13%, 3/1/29 (a)		375		377
6.38%, 6/1/24		250		258
Waste Pro USA, Inc.
5.50%, 2/15/26 (a)		475		482
Watco Cos. LLC/Watco Finance Corp.
6.50%, 6/15/27 (a)		750		769
WESCO Distribution, Inc.
7.13%, 6/15/25 (a)		250		273
XPO Logistics, Inc.
6.25%, 5/1/25 (a)		300		321
				30,915
Technology (3.1%)
Black Knight InfoServ LLC
3.63%, 9/1/28 (a)		350		354
Boxer Parent Co., Inc.
7.13%, 10/2/25 (a)		725		775
BY Crown Parent LLC
7.38%, 10/15/24 (a)		428		436
CDK Global, Inc.
5.25%, 5/15/29 (a)		250		266
Change Healthcare Holdings LLC/Change Healthcare Finance, Inc.
5.75%, 3/1/25 (a)		500		508
Diebold Nixdorf, Inc.,
8.50%, 4/15/24		350		320
9.38%, 7/15/25 (a)		325		344
IQVIA, Inc.
5.00%, 5/15/27 (a)		250		263
j2 Cloud Services LLC/j2 Global Co-Obligor, Inc.
6.00%, 7/15/25 (a)		750		781
MSCI, Inc.
4.75%, 8/1/26 (a)		150		156
MTS Systems Corp.
5.75%, 8/15/27 (a)		750		741

The accompanying notes are an integral part of the financial statements.
12

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

High Yield Portfolio

	Face Amount (000)		Value (000)
Technology (cont'd)
ON Semiconductor Corp.
3.88%, 9/1/28 (a)	$	325	$	330
Rackspace Hosting, Inc.
8.63%, 11/15/24 (a)		500		524
				5,798
Utilities (1.0%)
Calpine Corp.
5.00%, 2/1/31 (a)		300		307
LBC Tank Terminals Holding Netherlands BV
6.88%, 5/15/23 (a)		950		946
PG&E Corp.
5.25%, 7/1/30		600		581
				1,834
				173,757
Variable Rate Senior Loan Interests (3.2%)
Communication Services (0.2%)
CommScope, Inc.,
2019 Term B 1 Month USD LIBOR + 3.25%, 3.40%, 4/6/26 (f)		347		339
Connect Finco Sarl,
Term Loan B 1 Month USD LIBOR + 4.50%, 4.65%, 12/11/26 (f)		1		1
				340
Communications (0.4%)
Terrier Media Buyer, Inc.,
Term B 1 Month USD LIBOR + 4.25%, 4.40%, 12/17/26 (f)		703		688
Consumer, Cyclical (0.9%)
Playa Resorts Holding BV,
2017 Term Loan B 3 Month USD LIBOR + 2.75%, 3.75%, 4/29/24 (f)		630		558
Thor Industries, Inc.,
Term B 3 Month USD LIBOR + 3.75%, 3.94%, 2/1/26 (f)		629		627
Topgolf International, Inc.,
Term B 3 Month USD LIBOR + 6.25%, 7.00%, 2/8/26 (f)		493		485
				1,670
Consumer, Non-Cyclical (0.3%)
H Food Holdings LLC,
2018 Term Loan B 1 Month USD LIBOR + 3.68%, 3.83%, 5/23/25 (f)		660		643
Energy (0.0%)
Gavilan Resources LLC,
2nd Lien Term 3 Month USD LIBOR + 6.00%, 7.00%, 3/1/24 (d)(e)		1,000		13
Industrials (1.1%)
Airxcel, Inc.,
1st Lien Term 3 Month USD LIBOR + 4.50%, 4.69%, 4/28/25 (f)		634		599

	Face Amount (000)		Value (000)
Associated Asphalt Partners LLC,
Term B
3 Month USD LIBOR + 5.25%, 6.25%, 4/5/24 (f)	$	966	$	783
SAExploration Holdings, Inc.,
Term Loan Fixed + 10.00%, 1/4/21 (d)(e)		500		75
Titan Acquisition Limited,
2018 Term Loan B 3 Month USD LIBOR + 3.00%, 3.22%, 3/28/25 (f)		511		485
				1,942
Technology (0.3%)
DynCorp International, Inc.,
2019 Term Loan B 1 Month USD LIBOR + 6.00%, 7.00%, 8/18/25 (f)		570		568
				5,864
Total Fixed Income Securities (Cost $182,168)				179,621
	Shares
Common Stocks (0.2%)
Auto Components (0.0%)
Exide Technologies (g)		592		0
Equity Real Estate Investment Trusts (REITs) (0.1%)
American Gilsonite Co. (g)		500		200
Machinery (0.0%)
Iracore International Holdings, Inc., Class A (g)(h)		470		60
Semiconductors & Semiconductor Equipment (0.0%)
UC Holdings, Inc. (g)		2,826		29
Transportation (0.1%)
Sycreon Group BV/Syncreon Global Finance US, Inc. (g)		1,441		66
Total Common Stocks (Cost $151)				355
	No. of Warrants
Warrant (0.0%)
Transportation (0.0%)
Sncreon Group BV/Syncreon Global Finance US, Inc. expires 10/2/24 (Cost $—)		2,266		35
	Shares
Short-Term Investment (0.6%)
Investment Company (0.6%)
Morgan Stanley Institutional Liquidity Funds — Government Portfolio — Institutional Class (See Note G) (Cost $1,083)		1,083,228		1,083
Total Investments (98.6%) (Cost $183,402) (i)(j)				181,094
Other Assets in Excess of Liabilities (1.4%)				2,579
Net Assets (100.0%)			$	183,673

(a)  144A security — Certain conditions for public sale may exist. Unless otherwise noted, these securities are deemed to be liquid.

(b)  When-issued security.

(c)  PIK: Payment-in-kind security for which part of the income earned may be paid as additional principal.

The accompanying notes are an integral part of the financial statements.
13

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

High Yield Portfolio

(d)  Non-income producing security; bond in default.

(e)  Issuer in bankruptcy.

(f)  Floating or variable rate securities: The rates disclosed are as of September 30, 2020. For securities based on a published reference rate and spread, the reference rate and spread are indicated in the description in the Portfolio of Investments. Certain variable rate securities may not be based on a published reference rate and spread but are determined by the issuer or agent and are based on current market conditions. These securities do not indicate a reference rate and spread in their description in the Portfolio of Investments.

(g)  Non-income producing security.

(h)  At September 30, 2020, the Fund held a fair valued security valued at approximately $60,000 representing 0.03% of net assets. This security has been fair valued as determined in good faith under procedures established by and under the general supervision of the Trust's (as defined herein) Trustees.

(i)  Securities are available for collateral in connection with purchase of a when-issued securities.

(j)  At September 30, 2020, the aggregate cost for federal income tax purposes is approximately $183,785,000. The aggregate gross unrealized appreciation is approximately $5,300,000 and the aggregate gross unrealized depreciation is approximately $7,991,000, resulting in net unrealized depreciation of approximately $2,691,000.

LIBOR  London Interbank Offered Rate.

PIK  Payment-in-Kind. Income may be paid in additional securities or cash at the discretion of the issuer.

REITs  Real Estate Investment Trusts.

USD  United States Dollar.

Portfolio Composition

Classification	Percentage of Total Investments
Consumer, Cyclical		24.5	%
Industrials		17.2
Communications		12.5
Consumer, Non-Cyclical		12.4
Energy		10.7
Other*		9.1
Finance		7.9
Basic Materials		5.7
Total Investments		100.0	%

*  Industries and/or investment types representing less than 5% of total investments.

The accompanying notes are an integral part of the financial statements.
14

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

High Yield Portfolio

Statement of Assets and Liabilities	September 30, 2020 (000)
Assets:
Investments in Securities of Unaffiliated Issuers, at Value (Cost $182,319)	$	180,011
Investment in Security of Affiliated Issuer, at Value (Cost $1,083)		1,083
Total Investments in Securities, at Value (Cost $183,402)		181,094
Interest Receivable		3,136
Receivable for Investments Sold		1,256
Receivable for Fund Shares Sold		58
Receivable from Affiliate		—	@
Other Assets		55
Total Assets		185,599
Liabilities:
Payable for Investments Purchased		1,625
Payable for Professional Fees		82
Payable for Fund Shares Redeemed		72
Payable for Advisory Fees		62
Payable for Sub Transfer Agency Fees — Class I		20
Payable for Sub Transfer Agency Fees — Class A		4
Payable for Sub Transfer Agency Fees — Class L		—	@
Payable for Sub Transfer Agency Fees — Class C		1
Payable for Administration Fees		12
Payable for Shareholder Services Fees — Class A		3
Payable for Distribution and Shareholder Services Fees — Class L		—	@
Payable for Distribution and Shareholder Services Fees — Class C		6
Payable for Transfer Agency Fees — Class I		2
Payable for Transfer Agency Fees — Class A		1
Payable for Transfer Agency Fees — Class L		—	@
Payable for Transfer Agency Fees — Class C		1
Payable for Transfer Agency Fees — Class IS		1
Payable for Transfer Agency Fees — Class IR		—	@
Payable for Custodian Fees		4
Other Liabilities		30
Total Liabilities		1,926
Net Assets	$	183,673
Net Assets Consist of:
Paid-in-Capital	$	200,306
Total Accumulated Loss		(16,633	)
Net Assets	$	183,673

The accompanying notes are an integral part of the financial statements.
15

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

High Yield Portfolio

Statement of Assets and Liabilities (cont'd)	September 30, 2020 (000)
CLASS I:
Net Assets	$	155,539
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		16,931,014
Net Asset Value, Offering and Redemption Price Per Share	$	9.19
CLASS A:
Net Assets	$	14,595
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		1,591,636
Net Asset Value, Redemption Price Per Share	$	9.17
Maximum Sales Load		3.25	%
Maximum Sales Charge	$	0.31
Maximum Offering Price Per Share	$	9.48
CLASS L:
Net Assets	$	425
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		46,285
Net Asset Value, Offering and Redemption Price Per Share	$	9.17
CLASS C:
Net Assets	$	7,633
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		833,597
Net Asset Value, Offering and Redemption Price Per Share	$	9.16
CLASS IS:
Net Assets	$	5,471
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		595,345
Net Asset Value, Offering and Redemption Price Per Share	$	9.19
CLASS IR:
Net Assets	$	10
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		1,108
Net Asset Value, Offering and Redemption Price Per Share	$	9.19

@  Amount is less than $500.

The accompanying notes are an integral part of the financial statements.
16

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

High Yield Portfolio

Statement of Operations	Year Ended September 30, 2020 (000)
Investment Income:
Interest from Securities of Unaffiliated Issuers	$	13,021
Dividends from Security of Affiliated Issuer (Note G)		14
Total Investment Income		13,035
Expenses:
Advisory Fees (Note B)		1,142
Sub Transfer Agency Fees — Class I		188
Sub Transfer Agency Fees — Class A		28
Sub Transfer Agency Fees — Class L		—	@
Sub Transfer Agency Fees — Class C		4
Professional Fees		196
Administration Fees (Note C)		152
Shareholder Services Fees — Class A (Note D)		48
Distribution and Shareholder Services Fees — Class L (Note D)		2
Distribution and Shareholder Services Fees — Class C (Note D)		58
Registration Fees		96
Shareholder Reporting Fees		35
Pricing Fees		31
Transfer Agency Fees — Class I (Note E)		9
Transfer Agency Fees — Class A (Note E)		3
Transfer Agency Fees — Class L (Note E)		2
Transfer Agency Fees — Class C (Note E)		3
Transfer Agency Fees — Class IS (Note E)		2
Transfer Agency Fees — Class IR (Note E)		2
Custodian Fees (Note F)		16
Trustees' Fees and Expenses		8
Other Expenses		29
Expenses Before Non Operating Expenses		2,054
Bank Overdraft Expense		7
Total Expenses		2,061
Waiver of Advisory Fees (Note B)		(522	)
Reimbursement of Class Specific Expenses — Class I (Note B)		(150	)
Reimbursement of Class Specific Expenses — Class A (Note B)		(7	)
Reimbursement of Class Specific Expenses — Class L (Note B)		(2	)
Reimbursement of Class Specific Expenses — Class IS (Note B)		(2	)
Reimbursement of Class Specific Expenses — Class IR (Note B)		(2	)
Rebate from Morgan Stanley Affiliate (Note G)		(3	)
Net Expenses		1,373
Net Investment Income		11,662
Realized Loss:
Investments Sold		(12,570	)
Change in Unrealized Appreciation (Depreciation):
Investments		(417	)
Net Realized Loss and Change in Unrealized Appreciation (Depreciation)		(12,987	)
Net Decrease in Net Assets Resulting from Operations	$	(1,325	)

@  Amount is less than $500.

The accompanying notes are an integral part of the financial statements.
17

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

High Yield Portfolio

Statements of Changes in Net Assets	Year Ended September 30, 2020 (000)			Year Ended September 30, 2019 (000)
Increase (Decrease) in Net Assets:
Operations:
Net Investment Income	$	11,662		$	12,487
Net Realized Loss		(12,570	)		(1,825	)
Net Change in Unrealized Appreciation (Depreciation)		(417	)		(1,440	)
Net Increase (Decrease) in Net Assets Resulting from Operations		(1,325	)		9,222
Dividends and Distributions to Shareholders:
Class I		(10,175	)		(10,591	)
Class A		(1,185	)		(1,287	)
Class L		(25	)		(28	)
Class C		(300	)		(293	)
Class IS		(284	)		(54	)
Class IR		(1	)		(1	)
Total Dividends and Distributions to Shareholders		(11,970	)		(12,254	)
Capital Share Transactions:(1)
Class I:
Subscribed		47,804			86,572
Distributions Reinvested		10,167			10,572
Redeemed		(66,806	)		(68,177	)
Class A:
Subscribed		11,003			19,852
Distributions Reinvested		1,080			1,161
Redeemed		(19,692	)		(26,116	)
Class L:
Exchanged		—			5
Distributions Reinvested		25			27
Redeemed		(40	)		(58	)
Class C:
Subscribed		4,023			1,053
Distributions Reinvested		297			289
Redeemed		(1,823	)		(1,820	)
Class IS:
Subscribed		13,072			652
Distributions Reinvested		284			18
Redeemed		(9,316	)		(1,224	)
Class IR:
Distributions Reinvested		1			—	@
Net Increase (Decrease) in Net Assets Resulting from Capital Share Transactions		(9,921	)		22,806
Total Increase (Decrease) in Net Assets		(23,216	)		19,774
Net Assets:
Beginning of Period		206,889			187,115
End of Period	$	183,673		$	206,889

The accompanying notes are an integral part of the financial statements.
18

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

High Yield Portfolio

Statements of Changes in Net Assets (cont'd)	Year Ended September 30, 2020 (000)			Year Ended September 30, 2019 (000)
(1) Capital Share Transactions:
Class I:
Shares Subscribed		5,249			9,003
Shares Issued on Distributions Reinvested		1,101			1,094
Shares Redeemed		(7,471	)		(7,076	)
Net Increase (Decrease) in Class I Shares Outstanding		(1,121	)		3,021
Class A:
Shares Subscribed		1,208			2,058
Shares Issued on Distributions Reinvested		117			120
Shares Redeemed		(2,234	)		(2,721	)
Net Decrease in Class A Shares Outstanding		(909	)		(543	)
Class L:
Shares Exchanged		—			—	@@
Shares Issued on Distributions Reinvested		3			3
Shares Redeemed		(5	)		(6	)
Net Decrease in Class L Shares Outstanding		(2	)		(3	)
Class C:
Shares Subscribed		466			110
Shares Issued on Distributions Reinvested		32			30
Shares Redeemed		(201	)		(189	)
Net Increase (Decrease) in Class C Shares Outstanding		297			(49	)
Class IS:
Shares Subscribed		1,547			67
Shares Issued on Distributions Reinvested		32			2
Shares Redeemed		(1,014	)		(125	)
Net Increase (Decrease) in Class IS Shares Outstanding		565			(56	)
Class IR:
Shares Issued on Distributions Reinvested		—	@@		—	@@

@  Amount is less than $500.

@@  Amount is less than 500 shares.

The accompanying notes are an integral part of the financial statements.
19

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

High Yield Portfolio

	Class I
	Year Ended September 30,
Selected Per Share Data and Ratios	2020			2019			2018			2017			2016(1)
Net Asset Value, Beginning of Period	$	9.78		$	9.96		$	10.15		$	9.92		$	9.80
Income (Loss) from Investment Operations:
Net Investment Income(2)		0.57			0.63			0.65			0.70			0.67
Net Realized and Unrealized Gain (Loss)		(0.57	)		(0.19	)		(0.16	)		0.20			0.13
Total from Investment Operations		0.00			0.44			0.49			0.90			0.80
Distributions from and/or in Excess of:
Net Investment Income		(0.59	)		(0.62	)		(0.68	)		(0.67	)		(0.68	)
Net Asset Value, End of Period	$	9.19		$	9.78		$	9.96		$	10.15		$	9.92
Total Return(3)		0.15	%		4.68	%		5.01	%		9.40	%		8.72	%
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	155,539		$	176,483		$	149,683		$	64,007		$	49,990
Ratio of Expenses Before Expense Limitation		1.02	%		0.98	%		1.00	%		1.06	%		1.02	%
Ratio of Expenses After Expense Limitation		0.65	%(4)		0.65	%(4)		0.65	%(4)		0.66	%(4)		0.66	%(4)(5)
Ratio of Expenses After Expense Limitation Excluding Non-Operating Expenses		0.65	%(4)		0.65	%(4)		0.65	%(4)		0.65	%(4)		N/A
Ratio of Net Investment Income		6.20	%(4)		6.51	%(4)		6.49	%(4)		7.01	%(4)		7.09	%(4)(5)
Ratio of Rebate from Morgan Stanley Affiliates		0.00	%(6)		0.00	%(6)		0.00	%(6)		0.00	%(6)		0.00	%(6)
Portfolio Turnover Rate		69	%		42	%		39	%		73	%		74	%

(1)  Reflects prior period custodian out-of-pocket expenses that were reimbursed in September 2016. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class I shares. The Ratio of Expenses After Expense Limitation and the Ratio of Net Investment Income would be unchanged as the reimbursement of custodian fees was offset against expense waivers/reimbursements with no impact to net expenses or net investment income.

(2)  Per share amount is based on average shares outstanding.

(3)  Calculated based on the net asset value as of the last business day of the period.

(4)  The Ratio of Expenses After Expense Limitation and Ratio of Net Investment Income reflect the rebate of certain Fund expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates."

(5)  Effective January 4, 2016, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 0.65% for Class I shares. Prior to January 4, 2016, the maximum ratio was 0.75% for Class I shares.

(6) Amount is less than 0.005%.

The accompanying notes are an integral part of the financial statements.
20

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

High Yield Portfolio

	Class A
	Year Ended September 30,
Selected Per Share Data and Ratios	2020			2019			2018			2017			2016(1)
Net Asset Value, Beginning of Period	$	9.76		$	9.94		$	10.13		$	9.90		$	9.78
Income (Loss) from Investment Operations:
Net Investment Income(2)		0.55			0.60			0.61			0.67			0.64
Net Realized and Unrealized Gain (Loss)		(0.58	)		(0.20	)		(0.16	)		0.20			0.12
Total from Investment Operations		(0.03	)		0.40			0.45			0.87			0.76
Distributions from and/or in Excess of:
Net Investment Income		(0.56	)		(0.58	)		(0.64	)		(0.64	)		(0.64	)
Net Asset Value, End of Period	$	9.17		$	9.76		$	9.94		$	10.13		$	9.90
Total Return(3)		(0.22	)%		4.28	%		4.64	%		9.04	%		8.24	%
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	14,595		$	24,401		$	30,242		$	68,878		$	59,139
Ratio of Expenses Before Expense Limitation		1.31	%		1.23	%		1.29	%		1.34	%		1.33	%
Ratio of Expenses After Expense Limitation		1.00	%(4)		0.99	%(4)		1.00	%(4)		1.01	%(4)		1.02	%(4)(5)
Ratio of Expenses After Expense Limitation Excluding Non-Operating Expenses		1.00	%(4)		0.99	%(4)		1.00	%(4)		1.00	%(4)		N/A
Ratio of Net Investment Income		5.87	%(4)		6.17	%(4)		6.14	%(4)		6.65	%(4)		6.76	%(4)(5)
Ratio of Rebate from Morgan Stanley Affiliates		0.00	%(6)		0.00	%(6)		0.00	%(6)		0.00	%(6)		0.00	%(6)
Portfolio Turnover Rate		69	%		42	%		39	%		73	%		74	%

(1)  Reflects prior period custodian out-of-pocket expenses that were reimbursed in September 2016. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class A shares. The Ratio of Expenses After Expense Limitation and the Ratio of Net Investment Income would be unchanged as the reimbursement of custodian fees was offset against expense waivers/reimbursements with no impact to net expenses or net investment income.

(2)  Per share amount is based on average shares outstanding.

(3)  Calculated based on the net asset value which does not reflect sales charges, if applicable, as of the last business day of the period.

(4)  The Ratio of Expenses After Expense Limitation and Ratio of Net Investment Income reflect the rebate of certain Fund expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates."

(5)  Effective January 4, 2016, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 1.00% for Class A shares. Prior to January 4, 2016, the maximum ratio was 1.10% for Class A shares.

(6)  Amount is less than 0.005%.

The accompanying notes are an integral part of the financial statements.
21

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

High Yield Portfolio

	Class L
	Year Ended September 30,
Selected Per Share Data and Ratios	2020			2019			2018			2017			2016(1)
Net Asset Value, Beginning of Period	$	9.76		$	9.94		$	10.13		$	9.91		$	9.78
Income (Loss) from Investment Operations:
Net Investment Income(2)		0.52			0.57			0.59			0.64			0.62
Net Realized and Unrealized Gain (Loss)		(0.58	)		(0.19	)		(0.16	)		0.19			0.13
Total from Investment Operations		(0.06	)		0.38			0.43			0.83			0.75
Distributions from and/or in Excess of:
Net Investment Income		(0.53	)		(0.56	)		(0.62	)		(0.61	)		(0.62	)
Net Asset Value, End of Period	$	9.17		$	9.76		$	9.94		$	10.13		$	9.91
Total Return(3)		(0.46	)%		4.06	%		4.37	%		8.75	%		7.95	%
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	425		$	468		$	504		$	502		$	628
Ratio of Expenses Before Expense Limitation		1.91	%		1.86	%		1.91	%		1.90	%		1.83	%
Ratio of Expenses After Expense Limitation		1.25	%(4)		1.25	%(4)		1.25	%(4)		1.26	%(4)		1.28	%(4)(5)
Ratio of Expenses After Expense Limitation Excluding Non-Operating Expenses		1.25	%(4)		1.25	%(4)		1.25	%(4)		1.25	%(4)		N/A
Ratio of Net Investment Income		5.60	%(4)		5.93	%(4)		5.90	%(4)		6.40	%(4)		6.51	%(4)(5)
Ratio of Rebate from Morgan Stanley Affiliates		0.00	%(6)		0.00	%(6)		0.00	%(6)		0.00	%(6)		0.00	%(6)
Portfolio Turnover Rate		69	%		42	%		39	%		73	%		74	%

(1)  Reflects prior period custodian out-of-pocket expenses that were reimbursed in September 2016. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class L shares. The Ratio of Expenses After Expense Limitation and the Ratio of Net Investment Income would be unchanged as the reimbursement of custodian fees was offset against expense waivers/reimbursements with no impact to net expenses or net investment income.

(2)  Per share amount is based on average shares outstanding.

(3)  Calculated based on the net asset value as of the last business day of the period.

(4)  The Ratio of Expenses After Expense Limitation and Ratio of Net Investment Income reflect the rebate of certain Fund expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates."

(5)  Effective January 4, 2016, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 1.25% for Class L shares. Prior to January 4, 2016, the maximum ratio was 1.35% for Class L shares.

(6)  Amount is less than 0.005%.

The accompanying notes are an integral part of the financial statements.
22

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

High Yield Portfolio

	Class C
	Year Ended September 30,
Selected Per Share Data and Ratios	2020			2019			2018			2017			2016(1)
Net Asset Value, Beginning of Period	$	9.75		$	9.93		$	10.12		$	9.89		$	9.78
Income (Loss) from Investment Operations:
Net Investment Income(2)		0.46			0.52			0.54			0.59			0.57
Net Realized and Unrealized Gain (Loss)		(0.56	)		(0.19	)		(0.16	)		0.20			0.12
Total from Investment Operations		(0.10	)		0.33			0.38			0.79			0.69
Distributions from and/or in Excess of:
Net Investment Income		(0.49	)		(0.51	)		(0.57	)		(0.56	)		(0.58	)
Net Asset Value, End of Period	$	9.16		$	9.75		$	9.93		$	10.12		$	9.89
Total Return(3)		(0.93	)%		3.55	%		3.91	%		8.24	%		7.47	%
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	7,633		$	5,226		$	5,811		$	3,585		$	2,908
Ratio of Expenses Before Expense Limitation		2.02	%		1.98	%		2.01	%		2.09	%		2.12	%
Ratio of Expenses After Expense Limitation		1.74	%(4)		1.74	%(4)		1.73	%(4)		1.76	%(4)		1.77	%(4)(5)
Ratio of Expenses After Expense Limitation Excluding Non-Operating Expenses		1.74	%(4)		1.74	%(4)		1.73	%(4)		1.75	%(4)		N/A
Ratio of Net Investment Income		5.06	%(4)		5.43	%(4)		5.41	%(4)		5.90	%(4)		6.00	%(4)(5)
Ratio of Rebate from Morgan Stanley Affiliates		0.00	%(6)		0.00	%(6)		0.00	%(6)		0.00	%(6)		0.00	%(6)
Portfolio Turnover Rate		69	%		42	%		39	%		73	%		74	%

(1)  Reflects prior period custodian out-of-pocket expenses that were reimbursed in September 2016. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class C shares. The Ratio of Expenses After Expense Limitation and the Ratio of Net Investment Income would be unchanged as the reimbursement of custodian fees was offset against expense waivers/reimbursements with no impact to net expenses or net investment income.

(2)  Per share amount is based on average shares outstanding.

(3)  Calculated based on the net asset value which does not reflect sales charges, if applicable, as of the last business day of the period.

(4)  The Ratio of Expenses After Expense Limitation and Ratio of Net Investment Income reflect the rebate of certain Fund expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates."

(5)  Effective January 4, 2016, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 1.75% for Class C shares. Prior to January 4, 2016, the maximum ratio was 1.85% for Class C shares.

(6)  Amount is less than 0.005%.

The accompanying notes are an integral part of the financial statements.
23

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

High Yield Portfolio

	Class IS
	Year Ended September 30,
Selected Per Share Data and Ratios	2020			2019			2018			2017			2016(1)
Net Asset Value, Beginning of Period	$	9.78		$	9.96		$	10.15		$	9.92		$	9.79
Income (Loss) from Investment Operations:
Net Investment Income(2)		0.55			0.64			0.65			0.69			0.67
Net Realized and Unrealized Gain (Loss)		(0.55	)		(0.20	)		(0.16	)		0.21			0.14
Total from Investment Operations		0.00			0.44			0.49			0.90			0.81
Distributions from and/or in Excess of:
Net Investment Income		(0.59	)		(0.62	)		(0.68	)		(0.67	)		(0.68	)
Net Asset Value, End of Period	$	9.19		$	9.78		$	9.96		$	10.15		$	9.92
Total Return(3)		0.18	%		4.71	%		5.04	%		9.43	%		8.75	%
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	5,471		$	301		$	865		$	560		$	13,789
Ratio of Expenses Before Expense Limitation		0.94	%		1.11	%		1.15	%		0.99	%		0.93	%
Ratio of Expenses After Expense Limitation		0.62	%(4)		0.62	%(4)		0.62	%(4)		0.62	%(4)		0.62	%(4)(5)
Ratio of Expenses After Expense Limitation Excluding Non-Operating Expenses		0.62	%(4)		0.62	%(4)		0.62	%(4)		0.62	%(4)		N/A
Ratio of Net Investment Income		6.20	%(4)		6.55	%(4)		6.52	%(4)		6.93	%(4)		7.05	%(4)(5)
Ratio of Rebate from Morgan Stanley Affiliates		0.00	%(6)		0.00	%(6)		0.00	%(6)		0.00	%(6)		0.00	%(6)
Portfolio Turnover Rate		69	%		42	%		39	%		73	%		74	%

(1)  Reflects prior period custodian out-of-pocket expenses that were reimbursed in September 2016. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class IS shares. The Ratio of Expenses After Expense Limitation and the Ratio of Net Investment Income would be unchanged as the reimbursement of custodian fees was offset against expense waivers/reimbursements with no impact to net expenses or net investment income.

(2)  Per share amount is based on average shares outstanding.

(3)  Calculated based on the net asset value as of the last business day of the period.

(4)  The Ratio of Expenses After Expense Limitation and Ratio of Net Investment Income reflect the rebate of certain Fund expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates."

(5)  Effective January 4, 2016, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 0.62% for Class IS shares. Prior to January 4, 2016, the maximum ratio was 0.72% for Class IS shares.

(6)  Amount is less than 0.005%.

The accompanying notes are an integral part of the financial statements.
24

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

High Yield Portfolio

	Class IR
	Year Ended September 30,						Period from June 15, 2018(1) to
Selected Per Share Data and Ratios	2020			2019			September 30, 2018
Net Asset Value, Beginning of Period	$	9.78		$	9.96		$	9.93
Income (Loss) from Investment Operations:
Net Investment Income(2)		0.52			0.56			0.16
Net Realized and Unrealized Gain (Loss)		(0.52	)		(0.12	)		0.03
Total from Investment Operations		0.00			0.44			0.19
Distributions from and/or in Excess of:
Net Investment Income		(0.59	)		(0.62	)		(0.16	)
Net Asset Value, End of Period	$	9.19		$	9.78		$	9.96
Total Return(3)		0.18	%		4.71	%		1.92	%(6)
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period, (Thousands)	$	10		$	10		$	10
Ratio of Expenses Before Expense Limitation		20.43	%		20.17	%		18.62	%(7)
Ratio of Expenses After Expense Limitation		0.62	%(4)		0.62	%(4)		0.62	%(4)(7)
Ratios of Expenses After Expense Limitation Excluding Non-Operating Expenses		0.62	%(4)		0.62	%(4)		0.62	%(4)(7)
Ratio of Net Investment Income		5.70	%(4)		5.80	%(4)		5.75	%(4)(7)
Ratio of Rebate from Morgan Stanley Affiliates		0.00	%(5)		0.00	%(5)		0.00	%(5)(7)
Portfolio Turnover Rate		69	%		42	%		39	%(6)

(1)  Commencement of Offering

(2)  Per share amount is based on average shares outstanding

(3)  Calculated based on the net asset value as of the last business day of the period.

(4)  The Ratio of Expenses After Expense Limitation and Ratio of Net Investment Income reflect the rebate of certain Fund expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates

(5)  Amount is less than $0.005 per share.

(6)  Not annualized.

(7)  Annualized.

The accompanying notes are an integral part of the financial statements.
25

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements

Morgan Stanley Institutional Fund Trust ("Trust'') is registered under the Investment Company Act of 1940, as amended (the "Act"), as an open-end management investment company. The Trust is comprised of twelve separate, active funds (individually referred to as a "Fund," collectively as the "Funds"). The Trust applies investment company accounting and reporting guidance. All Funds are considered diversified for purposes of the Act.

The accompanying financial statements relate to the High Yield Portfolio. The Fund seeks total return. The Fund offers six classes of shares — Class I, Class A, Class L, Class C, Class IS and Class IR.

The Fund has suspended offering Class L shares for sale to all investors. Class L shareholders of the Fund do not have the option to purchasing additional Class L shares. However, existing Class L shareholders may invest in additional Class L shares through reinvestment of dividends and distributions.

A. Significant Accounting Policies: The following significant accounting policies are in conformity with U.S. generally accepted accounting principles ("GAAP"). Such policies are consistently followed by the Trust in the preparation of its financial statements. GAAP may require management to make estimates and assumptions that affect the reported amounts and disclosures in the financial statements. Actual results may differ from those estimates.

In March 2017, the Financial Accounting Standards Board ("FASB") issued an Accounting Standard Update, ASU 2017-08, Receivables-Nonrefundable Fees and Other Costs (Subtopic 310-20), Premium Amortization on Purchased Callable Debt Securities ("ASU 2017-08") which amends the amortization period for certain purchased callable debt securities held at a premium, shortening such period to the earliest call date. ASU 2017-08 does not require any accounting change for debt securities held at a discount; the discount continues to be accreted to maturity. ASU 2017-08 is effective for fiscal years, and interim periods within those fiscal years, beginning after December 15, 2018. The adoption resulted in a change in accounting principle, since the Fund had historically amortized such premiums to maturity for U.S. GAAP. Accordingly, the Fund has adopted ASU 2017-08 to amend the premium amortization period for certain purchased callable debt securities with non-contingent call features to the earliest call date. It is impracticable to evaluate the effect on individual prior periods, therefore the Fund applied the amendments on a modified retrospective basis by recognizing a cumulative effect adjustment

that decreased the beginning of period cost of investments and increased the unrealized appreciation on investments of approximately $84,000.

This change in accounting policy has been made to comply with the newly issued accounting standard and had no impact on total accumulated earnings (loss) or the net asset value of the Fund. With respect to the Fund's results of operations, amortization of premium to first call date accelerates amortization with the intent of more closely aligning the recognition of income on such bonds with the economics of the instrument.

In March 2020, FASB issued an Accounting Standard Update, ASU 2020-04, Reference Rate Reform (Topic 848) — Facilitation of the Effects of Reference Rate Reform on Financial Reporting ("ASU 2020-04"), which provides optional, temporary relief with respect to the financial reporting of contracts subject to certain types of modifications due to the planned discontinuation of the London Interbank Offered Rate ("LIBOR") and other IBOR-based reference rates at the end of 2021. The temporary relief provided by ASU 2020-04 is effective for certain reference rate-related contract modifications that occur during the period from March 12, 2020 through December 31, 2022. Management is evaluating the impact of ASU 2020-04 on the Fund's investments, derivatives, debt and other contracts that will undergo reference rate-related modifications as a result of the reference rate reform.

1.  Security Valuation: (1) Certain portfolio securities may be valued by an outside pricing service/vendor approved by the Trust's Board of Trustees (the "Trustees"). The pricing service/vendor may employ a pricing model that takes into account, among other things, bids, yield spreads and/or other market data and specific security characteristics. Alternatively, if a valuation is not available from an outside pricing service/vendor, and the security trades on an exchange, the security may be valued at its latest reported sale price (or at the exchange official closing price if such exchange reports an official closing price), prior to the time when assets are valued. If there are no sales on a given day and if there is no official exchange closing price for that day, the security is valued at the mean between the last reported bid and asked prices if such bid and asked prices are available in the relevant exchanges. If only bid prices are available then the latest bid price may be used. If Morgan Stanley Investment Management Inc. (the "Adviser"), a wholly-owned subsidiary of Morgan Stanley, determines that the price provided by the outside pricing service/vendor or exchange does not reflect the security's

26

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

fair value or is unable to provide a price, prices from brokers or dealers may also be utilized. In these circumstances, the value of the security will be the mean of bid and asked prices obtained from brokers or dealers; (2) an equity portfolio security listed or traded on an exchange is valued at its latest reported sales price (or at the exchange official closing price if such exchange reports an official closing price), and if there were no sales on a given day and if there is no official exchange closing price for that day, the security is valued at the mean between the last reported bid and asked prices if such bid and asked prices are available on the relevant exchanges. If only bid prices are available then the latest bid price may be used. Listed equity securities not traded on the valuation date with no reported bid and asked prices available on the exchange are valued at the mean between the current bid and asked prices obtained from one or more reputable brokers or dealers. In cases where a security is traded on more than one exchange, the security is valued on the exchange designated as the primary market; (3) all other equity portfolio securities for which over-the-counter ("OTC") market quotations are readily available are valued at the latest reported sales price (or at the market official closing price if such market reports an official closing price), and if there was no trading in the security on a given day and if there is no official closing price from relevant markets for that day, the security is valued at the mean between the last reported bid and asked prices if such bid and asked prices are available on the relevant markets. An unlisted equity security that does not trade on the valuation date and for which bid and asked prices from the relevant markets are unavailable is valued at the mean between the current bid and asked prices obtained from one or more reputable brokers or dealers; (4) certain senior collateralized loans ("Senior Loans") are valued based on quotations received from an independent pricing service; (5) when market quotations are not readily available, including circumstances under which the Adviser determines that the closing price, last sale price or the mean between the last reported bid and asked prices are not reflective of a security's market value, portfolio securities are valued at their fair value as determined in good faith under procedures established by and under the general supervision of the Trustees. Occasionally, developments affecting the closing prices of securities and other assets may occur between the times at which valuations of such securities are determined (that is, close of the foreign market on which the securities

trade) and the close of business of the New York Stock Exchange ("NYSE"). If developments occur during such periods that are expected to materially affect the value of such securities, such valuations may be adjusted to reflect the estimated fair value of such securities as of the close of the NYSE, as determined in good faith by the Trustees or by the Adviser using a pricing service and/or procedures approved by the Trustees; and (6) investments in mutual funds, including the Morgan Stanley Institutional Liquidity Funds, are valued at the net asset value ("NAV") as of the close of each business day.

The Trustees have responsibility for determining in good faith the fair value of the investments, and the Trustees may appoint others, such as the Trust's Adviser or a valuation committee, to assist the Trustees in determining fair value and to make the actual calculations pursuant to the fair valuation methodologies previously approved by the Trustees. Under procedures approved by the Trustees, the Trust's Adviser has formed a Valuation Committee whose members are approved by the Trustees. The Valuation Committee provides administration and oversight of the Trust's valuation policies and procedures, which are reviewed at least annually by the Trustees. These procedures allow the Trust to utilize independent pricing services, quotations from securities and financial instrument dealers and other market sources to determine fair value.

2.  Fair Value Measurement: FASB Accounting Standards Codification^TM ("ASC") 820, "Fair Value Measurement" ("ASC 820"), defines fair value as the value that the Fund would receive to sell an investment or pay to transfer a liability in a timely transaction with an independent buyer in the principal market, or in the absence of a principal market, the most advantageous market for the investment or liability. ASC 820 establishes a three-tier hierarchy to distinguish between (1) inputs that reflect the assumptions market participants would use in valuing an asset or liability developed based on market data obtained from sources independent of the reporting entity (observable inputs) and (2) inputs that reflect the reporting entity's own assumptions about the assumptions market participants would use in valuing an asset or liability developed based on the best information available in the circumstances (unobservable inputs) and to establish classification of fair value measurements for disclosure purposes. Various inputs are used in determining the value of

27

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

the Fund's investments. The inputs are summarized in the three broad levels listed below:

•  Level 1 – unadjusted quoted prices in active markets for identical investments

•  Level 2 – other significant observable inputs (including quoted prices for similar investments, interest rates, prepayment speeds, credit risk, etc.)

•  Level 3 – significant unobservable inputs including the Fund's own assumptions in determining the fair value of investments. Factors considered in making this determination may include, but are not limited to, information obtained by contacting the issuer, analysts, or the appropriate stock exchange (for exchange-traded securities), analysis of the issuer's financial statements or other available documents and, if necessary, available information concerning other securities in similar circumstances.

The inputs or methodology used for valuing securities are not necessarily an indication of the risk associated with investing in those securities and the determination of the significance of a particular input to the fair value measurement in its entirety requires judgment and considers factors specific to each security.

The following is a summary of the inputs used to value the Fund's investments as of September 30, 2020:

Investment Type	Level 1 Unadjusted quoted prices (000)		Level 2 Other significant observable inputs (000)		Level 3 Significant unobservable inputs (000)		Total (000)
Assets:
Fixed Income Securities
Corporate Bonds	$	—	$	173,757	$	—	$	173,757
Variable Rate Senior Loan Interests		—		5,864		—		5,864
Total Fixed Income Securities		—		179,621		—		179,621

Investment Type	Level 1 Unadjusted quoted prices (000)		Level 2 Other significant observable inputs (000)			Level 3 Significant unobservable inputs (000)		Total (000)
Common Stocks
Auto Components	$	—	$	—	†	$	—	$	—	†
Equity Real Estate Investment Trusts (REITs)		—		200			—		200
Machinery		—		—			60		60
Semiconductors & Semiconductor Equipment		—		29			—		29
Transportation		—		66			—		66
Total Common Stocks		—		295	†		60		355	†
Warrant		—		35			—		35
Short-Term Investment
Investment Company		1,083		—			—		1,083
Total Assets	$	1,083	$	179,951	†	$	60	$	181,094	†

†  Includes a security valued at zero.

Transfers between investment levels may occur as the markets fluctuate and/or the availability of data used in an investment's valuation changes.

Following is a reconciliation of investments in which significant unobservable inputs (Level 3) were used in determining fair value:

	Common Stock (000)
Beginning Balance	$	—
Purchases		—
Sales		—
Amortization of discount		—
Transfers in		—
Transfers out		—
Corporate actions		—
Change in unrealized appreciation (depreciation)		60
Realized gains (losses)		—
Ending Balance	$	60
Net change in unrealized appreciation (depreciation) from investments still held as of September 30, 2020	$	60

28

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

The following table presents additional information about valuation techniques and inputs used for investments that are measured at fair value and categorized within Level 3 as of September 30, 2020:

	Fair Value at September 30, 2020 (000)		Valuation Technique	Unobservable Input	Amount*			Impact to Valuation from an Increase in Input**
Common Stock		$60	Market Comparable Companies	Enterprise Value/ EBITDA		5.1x		Increase
				Discount for Lack of Marketability		40.0	%	Decrease

*  Amount is indicative of the weighted average.

**  Represents the expected directional change in the fair value of the Level 3 investments that would result from an increase in the corresponding input. A decrease to the unobservable input would have the opposite effect. Significant changes in these inputs could result in significantly higher or lower fair value measurements.

3.  Senior Loans: Senior Loans are typically structured by a syndicate of lenders ("Lenders"), one or more of which administers the Senior Loan on behalf of the Lenders ("Agent"). Lenders may sell interests in Senior Loans to third parties ("Participations") or may assign all or a portion of their interest in a Senior Loan to third parties ("Assignments"). Senior Loans are exempt from registration under the Securities Act of 1933. Presently, Senior Loans are not readily marketable and are often subject to restrictions on resale.

4.  Structured Investments: The Fund invested a portion of its assets in structured investments. A structured investment is a derivative security designed to offer a return linked to a particular underlying security, currency, commodity or market. Structured investments may come in various forms including notes (such as exchange-traded notes), warrants and options to purchase securities. The Fund will typically use structured investments to gain exposure to a permitted underlying security, currency, commodity or market when direct access to a market is limited or inefficient from a tax or cost standpoint. There can be no assurance that structured investments will trade at the same price or have the same value as the underlying security, currency, commodity or market. Investments in structured investments involve risks including issuer risk, counterparty risk and market risk. Holders of structured investments bear risks of the underlying investment and are subject to issuer or counterparty risk because the Fund is relying on the creditworthiness of such issuer or counterparty and has no rights with respect to the underlying investment. Certain structured investments may be thinly traded or have a limited trading market and may have the effect of increasing the Fund's illiquidity to the extent that

the Fund, at a particular time, may be unable to find qualified buyers for these securities.

5.  When-Issued/Delayed Delivery Securities: The Fund purchases and sells when-issued and delayed delivery securities. Securities purchased on a when-issued or delayed delivery basis are purchased for delivery beyond the normal settlement date at a stated price and yield, and no income accrues to the Fund on such securities prior to delivery date. Payment and delivery for when-issued and delayed delivery securities can take place a month or more after the date of the transaction. When the Fund enters into a purchase transaction on a when-issued or delayed delivery basis, securities are available for collateral in an amount at least equal in value to the Fund's commitments to purchase such securities. Purchasing securities on a when-issued or delayed delivery basis may involve a risk that the market price at the time of delivery may be lower than the agreed upon purchase price, in which case there could be an unrealized loss at the time of delivery. Purchasing investments on a when-issued or delayed delivery basis may be considered a form of leverage which may increase the impact that gains (losses) may have on the Fund.

6.  Indemnifications: The Trust enters into contracts that contain a variety of indemnifications. The Trust's maximum exposure under these arrangements is unknown. However, the Trust has not had prior claims or losses pursuant to these contracts and expects the risk of loss to be remote.

7.  Dividends and Distributions to Shareholders: Dividends and distributions to shareholders are recorded on the ex-dividend date. Dividends from net investment

29

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

income, if any, are declared and paid monthly. Net realized capital gains, if any, are distributed at least annually.

8.  Security Transactions, Income and Expenses: Security transactions are accounted for on the trade date (date the order to buy or sell is executed). Realized gains and losses on the sale of investment securities are determined on the specific identified cost method. When the Fund buys an interest in a Senior Loan, it may receive a commitment fee which is paid to lenders on an ongoing basis based upon the undrawn portion committed by the lenders of the underlying Senior Loan. The Fund accrues the commitment fee over the expected term of the loan. When the Fund sells an interest in a Senior Loan, it may be required to pay fees or commissions to the purchaser of the interest. Fees received in connection with loan amendments are accrued as earned. Dividend income and other distributions are recorded on the ex-dividend date (except for certain foreign dividends which may be recorded as soon as the Fund is informed of such dividends) net of applicable withholding taxes. Interest income is recognized on the accrual basis except where collection is in doubt. Discounts are accreted and premiums are amortized over the life of the respective securities. Most expenses of the Fund can be directly attributed to a particular Fund. Expenses which cannot be directly attributed are apportioned among the Funds based upon relative net assets or other appropriate methods. Income, expenses (other than class specific expenses — distribution and shareholder services, transfer agency and sub transfer agency fees) and realized and unrealized gains or losses are allocated to each class of shares based upon their relative net assets.

The Fund owns shares of real estate investment trusts ("REITs") which report information on the source of their distributions annually in the following calendar year. A portion of distributions received from REITs during the year is estimated to be a return of capital and is recorded as a reduction of their cost.

B. Advisory Fees: The Adviser, a wholly-owned subsidiary of Morgan Stanley, provides the Fund with advisory services under the terms of an Investment Advisory Agreement, paid quarterly, at an annual rate of 0.60% of the average daily net assets of the Fund.

The Adviser has agreed to reduce its advisory fee and/or reimburse the Fund so that total annual Fund operating expenses,

excluding certain investment related expenses, taxes, interest and other extraordinary expenses (including litigation), will not exceed 0.65% for Class I shares, 1.00% for Class A shares, 1.25% for Class L shares, 1.75% for Class C shares, 0.62% for Class IS shares and 0.62% for Class IR shares. The fee waivers and/or expense reimbursements will continue for at least one year from the date of the Fund's prospectus or until such time as the Trustees act to discontinue all or a portion of such waivers and/or reimbursements when they deem such action is appropriate. For the year ended September 30, 2020, approximately $522,000 of advisory fees were waived and approximately $163,000 of other expenses were reimbursed by the Adviser pursuant to this arrangement.

C. Administration Fees: The Adviser also serves as Administrator to the Trust and provides administrative services pursuant to an Administration Agreement for an annual fee, accrued daily and paid monthly, of 0.08% of the Fund's average daily net assets. Under a Sub-Administration Agreement between the Administrator and State Street Bank and Trust Company ("State Street"), State Street provides certain administrative services to the Trust. For such services, the Administrator pays State Street a portion of the fee the Administrator receives from the Fund.

D. Distribution and Shareholder Services Fees: Morgan Stanley Distribution, Inc. ("MSDI" or the "Distributor"), a wholly-owned subsidiary of the Adviser, and an indirect subsidiary of Morgan Stanley, serves as the Trust's Distributor of Fund shares pursuant to a Distribution Agreement. The Trust has adopted a Shareholder Services Plan with respect to Class A shares pursuant to Rule 12b-1 under the Act. Under the Shareholder Services Plan, the Fund pays the Distributor a shareholder services fee, accrued daily and paid monthly, at an annual rate of 0.25% of the Fund's average daily net assets attributable to Class A shares.

The Trust has adopted a Distribution and Shareholder Services Plan with respect to Class L shares pursuant to Rule 12b-1 under the Act. Under the Distribution and Shareholder Services Plan, the Fund pays the Distributor a distribution fee, accrued daily and paid monthly, at an annual rate of 0.25% and a shareholder services fee, accrued daily and paid monthly, at an annual rate of 0.25% of the Fund's average daily net assets attributable to Class L shares.

The Trust has adopted a Distribution and Shareholder Services Plan with respect to Class C shares pursuant to Rule 12b-1

30

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

under the Act. Under the Distribution and Shareholder Services Plan, the Fund pays the Distributor a distribution fee, accrued daily and paid monthly, at an annual rate of 0.75% and a shareholder services fee, accrued daily and paid monthly, at an annual rate of 0.25% of the Fund's average daily net assets attributable to Class C shares.

The distribution and shareholder services fees are used to support the expenses associated with servicing and maintaining accounts. The Distributor may compensate other parties for providing shareholder support services to investors who purchase Class A, Class L and Class C shares.

E. Dividend Disbursing and Transfer Agent: The Trust's dividend disbursing and transfer agent is DST Asset Manager Solutions, Inc. ("DST"). Pursuant to a Transfer Agency Agreement, the Trust pays DST a fee based on the number of classes, accounts and transactions relating to the Funds of the Trust.

F. Custodian Fees: State Street (the "Custodian") also serves as Custodian for the Trust in accordance with a Custodian Agreement. The Custodian holds cash, securities, and other assets of the Trust as required by the Act. Custody fees are payable monthly based on assets held in custody, investment purchases and sales activity and account maintenance fees, plus reimbursement for certain out-of-pocket expenses.

G. Security Transactions and Transactions with Affiliates: For the year ended September 30, 2020, purchases and sales of investment securities for the Fund, other than long-term U.S. Government securities and short-term investments were approximately $130,680,000 and $142,764,000, respectively. There were no purchases and sales of long-term U.S. Government securities for the year ended September 30, 2020.

The Fund invests in the Institutional Class of the Morgan Stanley Institutional Liquidity Funds — Government Portfolio (the "Liquidity Funds"), an open-end management investment company managed by the Adviser. Advisory fees paid by the Fund are reduced by an amount equal to its pro-rata share of the advisory and administration fees paid by the Fund due to its investment in the Liquidity Funds. For the year ended September 30, 2020, advisory fees paid were reduced by approximately $3,000 relating to the Fund's investment in the Liquidity Funds.

A summary of the Fund's transactions in shares of affiliated investments during the year ended September 30, 2020 is as follows:

Affiliated Investment Company	Value September 30, 2019 (000)		Purchases at Cost (000)		Proceeds from Sales (000)		Dividend Income (000)
Liquidity Funds	$	—	$	76,179	$	75,096	$	14

Affiliated Investment Company (cont'd)	Realized Gain (Loss) (000)		Change in Unrealized Appreciation (Depreciation) (000)		Value September 30, 2020 (000)
Liquidity Funds	$	—	$	—	$	1,083

The Fund is permitted to purchase and sell securities ("cross-trade") from and to other Morgan Stanley funds as well as other funds and client accounts for which the Adviser or an affiliate of the Adviser serves as investment adviser, pursuant to procedures approved by the Trustees in compliance with Rule 17a-7 under the Act (the "Rule"). Each cross-trade is executed at the current market price in compliance with provisions of the Rule. For the year ended September 30, 2020, the Fund did not engage in any cross-trade transactions.

The Fund has an unfunded Deferred Compensation Plan (the "Compensation Plan"), which allows each independent Trustee to defer payment of all, or a portion, of the fees he or she receives for serving on the Board of Trustees. Each eligible Trustee generally may elect to have the deferred amounts credited with a return equal to the total return on one or more of the Morgan Stanley funds that are offered as investment options under the Compensation Plan. Appreciation/depreciation and distributions received from these investments are recorded with an offsetting increase/decrease in the deferred compensation obligation and do not affect the NAV of the Fund.

H. Federal Income Taxes: It is the Fund's intention to continue to qualify as a regulated investment company and distribute all of its taxable and tax-exempt income. Accordingly, no provision for federal income taxes is required in the financial statements.

The Fund may be subject to taxes imposed by countries in which it invests. Such taxes are generally based on income and/or capital gains earned or repatriated. Taxes are accrued based on net investment income, net realized gains and net unrealized appreciation as such income and/or gains are earned. Taxes may also be based on transactions in foreign currency

31

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

and are accrued based on the value of investments denominated in such currency.

FASB ASC 740-10, "Income Taxes — Overall", sets forth a minimum threshold for financial statement recognition of the benefit of a tax position taken or expected to be taken in a tax return. Management has concluded there are no significant uncertain tax positions that would require recognition in the financial statements. If applicable, the Fund recognizes interest accrued related to unrecognized tax benefits in "Interest Expense" and penalties in "Other Expenses" in the Statement of Operations. The Fund files tax returns with the U.S. Internal Revenue Service, New York and various states. Generally, each of the tax years in the four-year period ended September 30, 2020 remains subject to examination by taxing authorities.

The tax character of distributions paid may differ from the character of distributions shown for GAAP purposes due to short-term capital gains being treated as ordinary income for tax purposes. The tax character of distributions paid during fiscal years 2020 and 2019 was as follows:

2020 Distributions Paid From: Ordinary Income (000)		2019 Distributions Paid From: Ordinary Income (000)
$	11,970	$	12,254

The amount and character of income and gains to be distributed are determined in accordance with income tax regulations which may differ from GAAP. These book/tax differences are either considered temporary or permanent in nature.

Temporary differences are attributable to differing book and tax treatments for the timing of the recognition of gains (losses) on certain investment transactions and the timing of the deductibility of certain expenses.

The Fund had no permanent differences causing reclassifications among the components of net assets for the year ended September 30, 2020.

At September 30, 2020, the components of distributable earnings for the Fund on a tax basis were as follows:

Undistributed Ordinary Income (000)		Undistributed Long-Term Capital Gain (000)
$	1,067	$	—

At September 30, 2020, the Fund had available for federal income tax purposes unused short-term and long-term capital losses of approximately $2,758,000 and $12,246,000, respectively, that do not have an expiration date.

To the extent that capital loss carryforwards are used to offset any future capital gains realized, no capital gains tax liability will be incurred by the Fund for gains realized and not distributed. To the extent that capital gains are offset, such gains will not be distributed to the shareholders.

I. Credit Facility: The Trust and other Morgan Stanley funds participated in a $300,000,000 committed, unsecured revolving line of credit facility (the "Facility") with State Street. This Facility is to be used for temporary emergency purposes or funding of shareholder redemption requests. The interest rate on borrowings is based on the federal funds rate or 1 month LIBOR rate plus a spread. The Facility also has a commitment fee of 0.25% per annum based on the unused portion of the Facility. During the year ended September 30, 2020, the Fund did not have any borrowings under the Facility.

J. Other: At September 30, 2020, the Fund had record owners of 10% or greater. Investment activities of these shareholders could have a material impact on the Fund. The aggregate percentage of such owners was 60.1%.

K. Market Risk: Certain impacts to public health conditions particular to the coronavirus (COVID-19) outbreak could impact the operations and financial performance of certain of the Fund's investments. The extent of the impact to the financial performance of the Fund's investments will depend on future developments, including (i) the duration and spread of the outbreak, (ii) the restrictions and advisories, (iii) the effects on the financial markets, and (iv) the effects on the economy overall, all of which are highly uncertain and cannot be predicted. If the financial performance of the Fund's investments is impacted because of these factors for an extended period, the Fund's investment results may be adversely affected.

L. LIBOR Risk: The Fund's investments, payment obligations and financing terms may be based on floating rates, such as London Interbank Offer Rate ("LIBOR"), Euro Interbank Offered Rate and other similar types of reference rates (each, a "Reference Rate"). These Reference Rates are generally intended to represent the rate at which contributing banks may obtain short-term borrowings from each other within certain financial markets. On July 27, 2017, the Chief Executive of the UK Financial Conduct Authority ("FCA"), which regulates LIBOR, announced that the FCA will no longer persuade nor require banks to submit rates for the calculation of LIBOR and certain other Reference Rates after 2021. Such announcement indicates that the continuation of LIBOR and other Reference

32

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

Rates on the current basis cannot and will not be guaranteed after the end of 2021. This announcement and any additional regulatory or market changes may have an adverse impact on the Fund or its investments.

In advance of 2022, regulators and market participants are currently engaged in identifying successor Reference Rates ("Alternative Reference Rates"). Additionally, prior to the end of 2021, it is expected that market participants will focus on the transition mechanisms by which the Reference Rates in existing contracts or instruments may be amended, whether through marketwide protocols, fallback contractual provisions,

bespoke negotiations or amendments or otherwise. Nonetheless, the termination of certain Reference Rates presents risks to the Fund. At this time, it is not possible to completely identify or predict the effect of any such changes, any establishment of Alternative Reference Rates or any other reforms to Reference Rates that may be enacted in the UK or elsewhere. The elimination of a Reference Rate or any other changes or reforms to the determination or supervision of Reference Rates could have an adverse impact on the market for or value of any securities or payments linked to those Reference Rates and other financial obligations held by the Fund or on its overall financial condition or results of operations.

33

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Report of Independent Registered Public Accounting Firm

To the Shareholders and Board of Trustees of
Morgan Stanley Institutional Fund Trust —
High Yield Portfolio

Opinion on the Financial Statements

We have audited the accompanying statement of assets and liabilities of High Yield Portfolio (the "Fund") (one of the funds constituting Morgan Stanley Institutional Fund Trust (the "Trust")), including the portfolio of investments, as of September 30, 2020, and the related statement of operations for the year then ended, the statements of changes in net assets for each of the two years in the period then ended, the financial highlights for each of the five years in the period then ended and the related notes (collectively referred to as the "financial statements"). In our opinion, the financial statements present fairly, in all material respects, the financial position of the Fund (one of the funds constituting Morgan Stanley Institutional Fund Trust) at September 30, 2020, the results of its operations for the year then ended, the changes in its net assets for each of the two years in the period then ended and its financial highlights for each of the five years in the period then ended, in conformity with U.S. generally accepted accounting principles.

Basis for Opinion

These financial statements are the responsibility of the Trust's management. Our responsibility is to express an opinion on the Fund's financial statements based on our audits. We are a public accounting firm registered with the Public Company Accounting Oversight Board (United States) ("PCAOB") and are required to be independent with respect to the Trust in accordance with the U.S. federal securities law and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB.

We conducted our audits in accordance with the standards of the PCAOB. Those standards require that we plan and perform the audit to obtain reasonable assurance about whether the financial statements are free of material misstatement, whether due to error or fraud. The Trust is not required to have, nor were we engaged to perform, an audit of the Trust's internal control over financial reporting. As part of our audits we are required to obtain an understanding of internal control over financial reporting but not for the purpose of expressing an opinion on the effectiveness of the Trust's internal control over financial reporting. Accordingly, we express no such opinion.

Our audits included performing procedures to assess the risks of material misstatement of the financial statements, whether due to error or fraud, and performing procedures that respond to those risks. Such procedures included examining, on a test basis, evidence regarding the amounts and disclosures in the financial statements. Our procedures included confirmation of securities owned as of September 30, 2020 by correspondence with the custodian and brokers or by other appropriate auditing procedures where replies from brokers were not received. Our audits also included evaluating the accounting principles used and significant estimates made by management, as well as evaluating the overall presentation of the financial statements. We believe that our audits provide a reasonable basis for our opinion.

We have served as the auditor of one or more Morgan Stanley investment companies since 2000.
Boston, Massachusetts
November 24, 2020

34

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Advisory Agreement Approval (unaudited)

Nature, Extent and Quality of Services

The Board reviewed and considered the nature and extent of the investment advisory services provided by the Adviser under the advisory agreement, including portfolio management, investment research and equity and fixed income securities trading. The Board also reviewed and considered the nature and extent of the non-advisory, administrative services provided by the Administrator under the administration agreement, including accounting, operations, clerical, bookkeeping, compliance, business management and planning, legal services and the provision of supplies, office space and utilities at the Adviser's expense. The Board also considered the Adviser's investment in personnel and infrastructure that benefits the Fund. (The Adviser and Administrator together are referred to as the "Adviser" and the advisory and administration agreements together are referred to as the "Management Agreement.") The Board also considered that the Adviser serves a variety of other investment advisory clients and has experience overseeing service providers. The Board also compared the nature of the services provided by the Adviser with similar services provided by non-affiliated advisers as prepared by Broadridge Financial Solutions, Inc. ("Broadridge").

The Board reviewed and considered the qualifications of the portfolio managers, the senior administrative managers and other key personnel of the Adviser who provide the advisory and administrative services to the Fund. The Board determined that the Adviser's portfolio managers and key personnel are well qualified by education and/or training and experience to perform the services in an efficient and professional manner. The Board concluded that the nature and extent of the advisory and administrative services provided were necessary and appropriate for the conduct of the business and investment activities of the Fund and supported its decision to approve the Management Agreement.

Performance, Fees and Expenses of the Fund

The Board reviewed the performance, fees and expenses of the Fund compared to its peers, as prepared by Broadridge, and to appropriate benchmarks where applicable. The Board discussed with the Adviser the performance goals and the actual results achieved in managing the Fund. When considering a fund's performance, the Board and the Adviser place emphasis on trends and longer-term returns (focusing on one-year, three-year and five-year performance, as of December 31, 2019, or since inception, as applicable). When a fund underperforms its benchmark and/or its peer group average, the Board and the Adviser discuss the causes of such underperformance and, where necessary, they discuss specific changes to investment strategy or investment personnel. The Board noted that the Fund's performance was better than its peer group average for the one-, three- and five-year periods. The Board discussed with the Adviser the level of the advisory and administration fees (together, the "management fee") for this Fund relative to comparable funds and/or other accounts advised by the Adviser and/or compared to its peers as prepared by Broadridge. In addition to the management fee, the Board also reviewed the Fund's total expense ratio. When a fund's management fee and/or its total expense ratio are higher than its peers, the Board and the Adviser discuss the reasons for this and, where appropriate, they discuss possible waivers and/or caps. The Board noted that the Fund's contractual management fee was higher than its peer group average and the actual management fee and total expense ratio were lower than its peer group averages. After discussion, the Board concluded that the Fund's performance, management fee and total expense ratio were competitive with its peer group averages.

Economies of Scale

The Board considered the size and growth prospects of the Fund and how that relates to the Fund's total expense ratio and particularly the Fund's management fee rate, which does not include breakpoints. In conjunction with its review of the Adviser's profitability, the Board discussed with the Adviser how a change in assets can affect the efficiency or effectiveness of managing the Fund and whether the management fee level is appropriate relative to current and projected asset levels and/or whether the management fee structure reflects economies of scale as asset levels change. The Board has determined that its review of the actual and/or potential economies of scale of the Fund supports its decision to approve the Management Agreement.

Profitability of the Adviser and Affiliates

The Board considered information concerning the costs incurred and profits realized by the Adviser and its affiliates during the last year from their relationship with the Fund and during the last two years from their relationship with the Morgan Stanley Fund Complex and reviewed with the Adviser the cost allocation methodology used to determine the profitability of the Adviser and affiliates. The Board has determined that its review of the analysis of the Adviser's expenses and profitability supports its decision to approve the Management Agreement.

35

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Advisory Agreement Approval (unaudited) (cont'd)

Other Benefits of the Relationship

The Board considered other direct and indirect benefits to the Adviser and/or its affiliates derived from their relationship with the Fund and other funds advised by the Adviser. These benefits may include, among other things, fees for trading, distribution and/or shareholder servicing and for transaction processing and reporting platforms used by securities lending agents, and research received by the Adviser generated from commission dollars spent on funds' portfolio trading. The Board reviewed with the Adviser these arrangements and the reasonableness of the Adviser's costs relative to the services performed. The Board has determined that its review of the other benefits received by the Adviser or its affiliates supports its decision to approve the Management Agreement.

Resources of the Adviser and Historical Relationship Between the Fund and the Adviser

The Board considered whether the Adviser is financially sound and has the resources necessary to perform its obligations under the Management Agreement. The Board also reviewed and considered the historical relationship between the Fund and the Adviser, including the organizational structure of the Adviser, the policies and procedures formulated and adopted by the Adviser for managing the Fund's operations and the Board's confidence in the competence and integrity of the senior managers and key personnel of the Adviser. The Board concluded that the Adviser has the financial resources necessary to fulfill its obligations under the Management Agreement and that it is beneficial for the Fund to continue its relationship with the Adviser.

Other Factors and Current Trends

The Board considered the controls and procedures adopted and implemented by the Adviser and monitored by the Fund's Chief Compliance Officer and concluded that the conduct of business by the Adviser indicates a good faith effort on its part to adhere to high ethical standards in the conduct of the Fund's business.

As part of the Board's review, the Board received information from management on the impact of COVID-19 on the firm generally and the Adviser and the Fund in particular including, among other information, the pandemic's current and expected impact on the Fund's performance and operations.

General Conclusion

After considering and weighing all of the above factors, with various written materials and verbal information presented by the Adviser, the Board concluded that it would be in the best interest of the Fund and its shareholders to approve renewal of the Management Agreement for another year. In reaching this conclusion the Board did not give particular weight to any single piece of information or factor referenced above. The Board considered these factors and information over the course of the year and in numerous meetings, some of which were in executive session with only the independent Board members and their counsel present. It is possible that individual Board members may have weighed these factors, and the information presented, differently in reaching their individual decisions to approve the Management Agreement.

36

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Liquidity Risk Management Program (unaudited)

In compliance with Rule 22e-4 under the Investment Company Act of 1940, as amended (the "Liquidity Rule"), the Fund has adopted and implemented a liquidity risk management program (the "Program"), which is reasonably designed to assess and manage the risk that the Fund could not meet requests to redeem shares issued by the Fund without significant dilution of remaining investors' interests in the Fund (i.e., liquidity risk). The Fund's Board of Trustees (the "Board") previously approved the designation of the Liquidity Risk Subcommittee (the "LRS") as Program administrator. The LRS is comprised of representatives from various divisions within Morgan Stanley Investment Management.

At a meeting held on April 22-23, 2020, the Board reviewed a written report prepared by the LRS that addressed the Program's operation and assessed its adequacy, and effectiveness of implementation for the period from December 1, 2018, through December 31, 2019, as required under the Liquidity Rule. The report concluded that the Program operated effectively and was adequately and effectively implemented in all material aspects, and that the relevant controls and safeguards were appropriately designed to enable the LRS to administer the Program in compliance with the Liquidity Rule.

In accordance with the Program, the LRS assessed each Fund's liquidity risk no less frequently than annually taking into consideration certain factors, as applicable, such as (i) investment strategy and liquidity of portfolio investments, (ii) short-term and long-term cash flow projections and (iii) holdings of cash and cash equivalents and borrowing arrangements and other funding sources. Certain factors are considered under both normal and reasonably foreseeable stressed conditions.

Each Fund portfolio investment is classified into one of four liquidity categories, which classification is assessed at least monthly by the LRS. The classification is based on a determination of the number of days it is reasonably expected to take to convert the investment into cash, or sell or dispose of the investment, in current market conditions without significantly changing the market value of the investment. Liquidity classification determinations take into account various market, trading and investment-specific considerations, as well as market depth, and in some cases utilize third-party vendor data.

The Liquidity Rule limits a fund's investments in illiquid investments to 15% of its net assets and requires funds that do not primarily hold assets that are highly liquid investments to determine and maintain a minimum percentage of the fund's net assets to be invested in highly liquid investments (highly liquid investment minimum or "HLIM"). The LRS believes that the Program includes provisions reasonably designed to review, monitor and comply with the 15% limit on illiquid investments and for determining, periodically reviewing and complying with the HLIM requirement, as applicable.

There can be no assurance that the Program will achieve its objectives under all circumstances in the future. Please refer to the Fund's prospectus for more information regarding the Fund's exposure to liquidity risk and other risks to which it may be subject.

37

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Privacy Notice (unaudited)  April 2019

FACTS	WHAT DOES MSIM DO WITH YOUR PERSONAL INFORMATION?
Why?	Financial companies choose how they share your personal information. Federal law gives consumers the right to limit some but not all sharing. Federal law also requires us to tell you how we collect, share, and protect your personal information. Please read this notice carefully to understand what we do.
What?	The types of personal information we collect and share depend on the product or service you have with us. This information can include: n Social Security number and income n investment experience and risk tolerance n checking account number and wire transfer instructions
How?	All financial companies need to share customers' personal information to run their everyday business. In the section below, we list the reasons financial companies can share their customers' personal information; the reasons MSIM chooses to share; and whether you can limit this sharing.

Reasons we can share your personal information	Does MSIM share?	Can you limit this sharing?
For our everyday business purposes — such as to process your transactions, maintain your account(s), respond to court orders and legal investigations, or report to credit bureaus	Yes	No
For our marketing purposes — to offer our products and services to you	Yes	No
For joint marketing with other financial companies	No	We don't share
For our affiliates' everyday business purposes — information about your transactions and experiences	Yes	No
For our affiliates' everyday business purposes — information about your creditworthiness	No	We don't share
For our affiliates to market to you	No	We don't share
For non-affiliates to market to you	No	We don't share

Questions?Call toll-free (844) 312-6327 or email: imprivacyinquiries@morganstanley.com

38

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Privacy Notice (unaudited) (cont'd)  April 2019

Who we are

Who is providing this notice? Morgan Stanley Investment Management, Inc. and its affiliated registered investment advisers, registered broker-dealers, and registered and unregistered funds ("MSIM")

What we do

How does MSIM protect my personal information?	To protect your personal information from unauthorized access and use, we use security measures that comply with federal law. These measures include computer safeguards and secured files and buildings. We have policies governing the proper handling of customer information by personnel and requiring third parties that provide support to adhere to appropriate security standards with respect to such information.
How does MSIM collect my personal information?	We collect your personal information, for example, when you n open an account or make deposits or withdrawals from your account n buy securities from us or make a wire transfer n give us your contact information We also collect your personal information from others, such as credit bureaus, affiliates, or other companies.
Why can't I limit all sharing?	Federal law gives you the right to limit only n sharing for affiliates' everyday business purposes — information about your creditworthiness n affiliates from using your information to market to you n sharing for non-affiliates to market to you State laws and individual companies may give you additional rights to limit sharing. See below for more on your rights under state law.

Definitions

Affiliates	Companies related by common ownership or control. They can be financial and non-financial companies. n Our affiliates include companies with a Morgan Stanley name and financial companies such as Morgan Stanley Smith Barney LLC and Morgan Stanley & Co.
Non-affiliates	Companies not related by common ownership or control. They can be financial and non-financial companies. n MSIM does not share with non-affiliates so they can market to you.
Joint marketing	A formal agreement between non-affiliated financial companies that together market financial products or services to you. n MSIM doesn't jointly market

Other Important Information

Vermont: Except as permitted by law, we will not share personal information we collect about Vermont residents with Non-affiliates unless you provide us with your written consent to share such information.

California: Except as permitted by law, we will not share personal information we collect about California residents with Non-affiliates and we will limit sharing such personal information with our Affiliates to comply with California privacy laws that apply to us.

39

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited)

Independent Trustees:

Name, Address and Birth Year of Independent Trustee	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years and Other Relevant Professional Experience	Number of Funds in Fund Complex Overseen by Independent Trustee**		Other Directorships Held by Independent Trustee***
Frank L. Bowman c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1944	Trustee	Since August 2006	President, Strategic Decisions, LLC (consulting) (since February 2009); Director or Trustee of various Morgan Stanley Funds (since August 2006); Chairperson of the Compliance and Insurance Committee (since October 2015); formerly, Chairperson of the Insurance Sub-Committee of the Compliance and Insurance Committee (2007-2015); served as President and Chief Executive Officer of the Nuclear Energy Institute (policy organization) (February 2005-November 2008); retired as Admiral, U.S. Navy after serving over 38 years on active duty including 8 years as Director of the Naval Nuclear Propulsion Program in the Department of the Navy and the U.S. Department of Energy (1996-2004); served as Chief of Naval Personnel (July 1994-September 1996) and on the Joint Staff as Director of Political Military Affairs (June 1992-July 1994); knighted as Honorary Knight Commander of the Most Excellent Order of the British Empire; awarded the Officier de l'Orde National du Mérite by the French Government; elected to the National Academy of Engineering (2009).		86	Director of Naval and Nuclear Technologies LLP; Director Emeritus of the Armed Services YMCA; Member of the National Security Advisory Council of the Center for U.S. Global Engagement and a member of the CNA Military Advisory Board; Trustee of Fairhaven United Methodist Church; Member of the Board of Advisors of the Dolphin Scholarship Foundation; Director of other various non-profit organizations; Formerly, Director of BP p.l.c. (November 2010-May 2019).
Kathleen A. Dennis c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1953	Trustee	Since August 2006	President, Cedarwood Associates (mutual fund and investment management consulting) (since July 2006); Chairperson of the Liquidity and Alternatives Sub-Committee of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 2006); formerly, Senior Managing Director of Victory Capital Management (1993-2006).		86	Director of various non-profit organizations.
Nancy C. Everett c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1955	Trustee	Since January 2015	Chief Executive Officer, Virginia Commonwealth University Investment Company (since November 2015); Owner, OBIR, LLC (institutional investment management consulting) (since June 2014); formerly, Managing Director, BlackRock, Inc. (February 2011-December 2013); and Chief Executive Officer, General Motors Asset Management (a/k/a Promark Global Advisors, Inc.) (June 2005-May 2010).		87	Formerly, Member of Virginia Commonwealth University School of Business Foundation (2005-2016); Member of Virginia Commonwealth University Board of Visitors (2013-2015); Member of Committee on Directors for Emerging Markets Growth Fund, Inc. (2007-2010); Chairperson of Performance Equity Management, LLC (2006-2010); and Chairperson, GMAM Absolute Return Strategies Fund, LLC (2006-2010).

40

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Address and Birth Year of Independent Trustee	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years and Other Relevant Professional Experience	Number of Funds in Fund Complex Overseen by Independent Trustee**		Other Directorships Held by Independent Trustee***
Jakki L. Haussler c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1957	Trustee	Since January 2015	Chairman, Opus Capital Group (since January 1996); formerly, Chief Executive Officer, Opus Capital Group (1996-2019); Director, Capvest Venture Fund, LP (May 2000-December 2011); Partner, Adena Ventures, LP (July 1999-December 2010); Director, The Victory Funds (February 2005-July 2008).		87	Director of Service Corporation International and Member, Audit Committee and Investment Committee; Director of Cincinnati Bell Inc. and Member, Audit Committee and Governance and Nominating Committee; Director of Northern Kentucky University Foundation and Member, Investment Committee; Member of Chase College of Law Transactional Law Practice Center Board of Advisors; Director of Chase College of Law Board of Visitors; formerly, Member, University of Cincinnati Foundation Investment Committee; Member, Miami University Board of Visitors (2008-2011); Trustee of Victory Funds (2005-2008) and Chairman, Investment Committee (2007-2008); Member, Service Provider Committee (2005-2008) and Director of Best Transport (2006-2019).
Dr. Manuel H. Johnson c/o Johnson Smick International, Inc. 220 I Street, NE — Suite 200 Washington, D.C. 20002 Birth Year 1949	Trustee	Since July 1991	Senior Partner, Johnson Smick International, Inc. (consulting firm); Chairperson of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since July 1991); Co-Chairman and a founder of the Group of Seven Council (G7C) (international economic commission); formerly, Chairperson of the Audit Committee (July 1991-September 2006), Vice Chairman of the Board of Governors of the Federal Reserve System and Assistant Secretary of the U.S. Treasury.		86	Director of NVR, Inc. (home construction).
Joseph J. Kearns c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1942	Trustee	Since August 1994	Senior Adviser, Kearns & Associates LLC (investment consulting); Chairperson of the Audit Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 1994); Director, Rubicorn Investments (since February 2019); formerly, Deputy Chairperson of the Audit Committee (July 2003-September 2006) and Chairperson of the Audit Committee of various Morgan Stanley Funds (since August 1994); CFO of the J. Paul Getty Trust (1982-1999).		87	Prior to August 10, 2016, Director of Electro Rent Corporation (equipment leasing); Prior to December 31, 2013, Director of The Ford Family Foundation.

41

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Address and Birth Year of Independent Trustee	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years and Other Relevant Professional Experience	Number of Funds in Fund Complex Overseen by Independent Trustee**		Other Directorships Held by Independent Trustee***
Michael F. Klein c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1958	Trustee	Since August 2006	Managing Director, Aetos Alternatives Management, LP (since March 2000); Co-President, Aetos Alternatives Management, LP (since January 2004) and Co-Chief Executive Officer of Aetos Alternatives Management, LP (since August 2013); Chairperson of the Fixed Income Sub-Committee of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 2006); formerly, Managing Director, Morgan Stanley & Co. Inc. and Morgan Stanley Dean Witter Investment Management and President, various Morgan Stanley Funds (June 1998-March 2000); Principal, Morgan Stanley & Co. Inc. and Morgan Stanley Dean Witter Investment Management (August 1997-December 1999).		86	Director of certain investment funds managed or sponsored by Aetos Alternatives Management, LP; Director of Sanitized AG and Sanitized Marketing AG (specialty chemicals).
Patricia Maleski c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1960	Trustee	Since January 2017	Managing Director, JPMorgan Asset Management (2004-2016); Oversight and Control Head of Fiduciary and Conflicts of Interest Program (2015-2016); Chief Control Officer-Global Asset Management (2013-2015); President, JPMorgan Funds (2010-2013); Chief Administrative Officer (2004-2013); various other positions including Treasurer and Board Liaison (since 2001).		87	None.
W. Allen Reed c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1947	Chair of the Board and Trustee	Chair of the Boards since August 2020 and Trustee since August 2006	Chair of the Boards of various Morgan Stanley Funds (since August 2020); Chairperson of the Governance Committee; Chairperson of the Equity Sub-Committee of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 2006); formerly, Vice Chair of the Boards of various Morgan Stanley Funds (January 2020-August 2020); President and Chief Executive Officer of General Motors Asset Management; Chairman and Chief Executive Officer of the GM Trust Bank and Corporate Vice President of General Motors Corporation (August 1994-December 2005).		86	Formerly, Director of Legg Mason, Inc. (2006-2019); and Director of the Auburn University Foundation (2010-2015).

*  This is the earliest date the Trustee began serving the Morgan Stanley Funds. Each Trustee serves an indefinite term, until his or her successor is elected.

**  The Fund Complex includes (as of December 31, 2019) all open-end and closed-end funds (including all of their portfolios) advised by Morgan Stanley Investment Management Inc. (the "Adviser") and any funds that have an adviser that is an affiliated person of the Adviser (including, but not limited to, Morgan Stanley AIP GP LP).

***  This includes any directorships at public companies and registered investment companies held by the Trustee at any time during the past five years.

42

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited) (cont'd)

Executive Officers:

Name, Address and Birth Year of Executive Officer	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years
John H. Gernon 522 Fifth Avenue New York, NY 10036 Birth Year 1963	President and Principal Executive Officer	Since September 2013	President and Principal Executive Officer of the Equity and Fixed Income Funds and the Morgan Stanley AIP Funds (since September 2013) and the Liquidity Funds and various money market funds (since May 2014) in the Fund Complex; Managing Director of the Adviser; Head of Public Markets Product Development (since 2006).
Timothy J. Knierim 522 Fifth Avenue New York, NY 10036 Birth Year 1959	Chief Compliance Officer	Since December 2016	Managing Director of the Adviser and various entities affiliated with the Adviser; Chief Compliance Officer of various Morgan Stanley Funds and the Adviser (since December 2016) and Chief Compliance Officer of Morgan Stanley AIP GP LP (since 2014). Formerly, Managing Director and Deputy Chief Compliance Officer of the Adviser (2014-2016); and formerly, Chief Compliance Officer of Prudential Investment Management, Inc. (2007-2014).
Francis J. Smith 522 Fifth Avenue New York, NY 10036 Birth Year 1965	Treasurer and Principal Financial Officer	Treasurer since July 2003 and Principal Financial Officer since September 2002	Managing Director of the Adviser and various entities affiliated with the Adviser; Treasurer (since July 2003) and Principal Financial Officer of various Morgan Stanley Funds (since September 2002).
Mary E. Mullin 522 Fifth Avenue New York, NY 10036 Birth Year 1967	Secretary	Since June 1999	Managing Director of the Adviser; Secretary of various Morgan Stanley Funds (since June 1999).
Michael J. Key 522 Fifth Avenue New York, NY 10036 Birth Year 1979	Vice President	Since June 2017	Vice President of the Equity and Fixed Income Funds, Liquidity Funds, various money market funds and the Morgan Stanley AIP Funds in the Fund Complex (since June 2017); Executive Director of the Adviser; Head of Product Development for Equity and Fixed Income Funds (since August 2013).

*  This is the earliest date the officer began serving the Morgan Stanley Funds. Each officer serves a one-year term, until his or her successor is elected and qualifies.

43

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Adviser and Administrator

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

Distributor

Morgan Stanley Distribution, Inc.
522 Fifth Avenue
New York, New York 10036

Dividend Disbursing and Transfer Agent

DST Asset Manager Solutions, Inc.
2000 Crown Colony Drive
Quincy, Massachusetts 02169

Custodian

State Street Bank and Trust Company
One Lincoln Street
Boston, Massachusetts 02111

Legal Counsel

Dechert LLP
1095 Avenue of the Americas
New York, New York 10036

Counsel to the Independent Trustees

Perkins Coie LLP
1155 Avenue of the Americas,
22nd Floor
New York, New York 10036

Independent Registered Public Accounting Firm

Ernst & Young LLP
200 Clarendon Street
Boston, Massachusetts 02116

Reporting to Shareholders

Each Morgan Stanley fund provides a complete schedule of portfolio holdings in its Semi-Annual and the Annual Reports within 60 days of the end of the fund's second and fourth fiscal quarters. The Semi-Annual and Annual Reports are filed electronically with the Securities and Exchange Commission ("SEC") on Form N-CSRS and Form N-CSR, respectively. Morgan Stanley also delivers the Semi-Annual and Annual Reports to fund shareholders and makes these reports available on its public website, www.morganstanley.com/im/shareholderreports. Each Morgan Stanley non-money market fund also files a complete schedule of portfolio holdings with the SEC for the fund's first and third fiscal quarters as an attachment to Form N-PORT. Morgan Stanley does not deliver the reports for the first and third fiscal quarters to shareholders, nor are the reports posted to the Morgan Stanley public website. However, the holdings for each money market fund are posted to the Morgan Stanley public website. You may obtain the Form N-PORT filings (as well as the Form N-CSR and N-CSRS filings) by accessing the SEC's website, www.sec.gov. You can also request copies of these materials, upon payment of a duplicating fee, by electronic request at the SEC's email address (publicinfo@sec.gov).

Proxy Voting Policies and Procedures and Proxy Voting Record

You may obtain a copy of the Trust's Proxy Voting Policy and Procedures and information regarding how the Trust voted proxies relating to portfolio securities during the most recent twelve-month period ended June 30, without charge, upon request, by calling toll free 1 (800) 548-7786 or by visiting our website at www.morganstanley.com/im/shareholderreports. This information is also available on the SEC's website at www.sec.gov.

This report is authorized for distribution only when preceded or accompanied by a prospectus or summary prospectus of the applicable fund of Morgan Stanley Institutional Fund Trust, which describes in detail the fund's investment policies, risks, fees and expenses. Please read the prospectus carefully before you invest or send money. For additional information, including information regarding the investments comprising the Fund, please visit our website at www.morganstanley.com/im/shareholderreports or call toll free 1 (800) 548-7786.

44

Printed in U.S.A.
This Report has been prepared for shareholders and may be distributed to others only if preceded or accompanied by a current prospectus.

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

© 2020 Morgan Stanley. Morgan Stanley Distribution, Inc.

IFTHYANN
3299130 EXP 11.30.21

INVESTMENT MANAGEMENT

Morgan Stanley Institutional Fund Trust

Intermediate Municipal Income Portfolio

Annual Report

September 30, 2020

Beginning on January 1, 2021, as permitted by regulations adopted by the Securities and Exchange Commission ("SEC"), paper copies of the Fund's Annual and Semi-Annual Reports to Shareholders ("Shareholder Reports") will no longer be sent by mail, unless you specifically request paper copies of the Shareholder Reports from the Fund or from your financial intermediary, such as a broker-dealer or a bank. Instead, the Shareholder Reports will be made available on the Fund's website, https://www.morganstanley.com/im/shareholderreports and you will be notified by mail each time a Shareholder Report is posted and provided with a website link to access the Shareholder Report. If you already elected to receive Shareholder Reports electronically, you will not be affected by this change and you need not take any action. You may elect to receive Shareholder Reports and other communications from the Fund electronically anytime by contacting your financial intermediary or, if you are a direct investor, please follow the instructions on the envelope.

Beginning on January 1, 2019, you may elect to receive all future Shareholder Reports in paper free of charge. If you invest through a financial intermediary, you can contact your financial intermediary to request that you continue to receive paper copies of your Shareholder Reports. If you invest directly with the Fund, please follow the instructions on the envelope to let the Fund know you wish to continue receiving paper copies of your Shareholder Reports. Your election to receive Shareholder Reports in paper will apply to all funds held in your account if you invest through your financial intermediary or all funds held with the fund complex if you invest directly with a fund.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Table of Contents

Shareholders' Letter	2
Expense Example	3
Investment Overview	4
Portfolio of Investments	5
Statement of Assets and Liabilities	7
Statement of Operations	8
Statement of Changes in Net Assets	9
Financial Highlights	10
Notes to Financial Statements	14
Report of Independent Registered Public Accounting Firm	19
Investment Advisory Agreement Approval	20
Liquidity Risk Management Program	22
Privacy Notice	23
Trustee and Officer Information	25

This report is authorized for distribution only when preceded or accompanied by a prospectus or summary prospectus of the applicable Fund of the Morgan Stanley Institutional Fund Trust. To receive a prospectus and/or statement of additional information ("SAI"), which contains more complete information such as investment objectives, charges, expenses, policies for voting proxies, risk considerations and describes in detail each of the Fund's investment policies to the prospective investor, please call toll free 1 (800) 548-7786. Please read the prospectuses carefully before you invest or send money.

Additionally, you can access information about the Fund, including performance, characteristics and investment team commentary, through Morgan Stanley Investment Management's website: www.morganstanley.com/im/shareholderreports.

Market forecasts provided in this report may not necessarily come to pass. There is no guarantee that any sectors mentioned will continue to perform as discussed herein or that securities in such sectors will be held by the Fund in the future. There is no assurance that a fund will achieve its investment objective. Funds are subject to market risk, which is the possibility that market values of securities owned by the Fund will decline and, therefore, the value of the Fund's shares may be less than what you paid for them. Accordingly, you can lose money investing in this Fund. Please see the prospectus for more complete information on investment risks.

1

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Shareholders' Letter (unaudited)

Dear Shareholders,

We are pleased to provide this Annual Report, in which you will learn how your investment in Intermediate Municipal Income Portfolio (the "Fund") performed during the period ended September 30, 2020 (when the Fund commenced operations).

Morgan Stanley Investment Management is a client-centric, investor-led organization. Our global presence, intellectual capital, and breadth of products and services enable us to partner with investors to meet the evolving challenges of today's financial markets. We aim to deliver superior investment service and to empower our clients to make the informed decisions that help them reach their investment goals.

As always, we thank you for selecting Morgan Stanley Investment Management, and look forward to working with you in the months and years ahead.

Sincerely,

John H. Gernon
President and Principal Executive Officer

October 2020

2

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Expense Example (unaudited)

Intermediate Municipal Income Portfolio

As a shareholder of the Fund, you may incur two types of costs: (1) transactional costs, including sales charge (loads) on purchase payments; and (2) ongoing costs, which may include advisory fees, administration fees, distribution and shareholder services fees; and other Fund expenses. This example is intended to help you understand your ongoing costs (in dollars) of investing in the Fund and to compare these costs with the ongoing costs of investing in other mutual funds.

This example is based on an investment of $1,000 invested at the beginning of the period and held for the entire period 9/30/20-9/30/20.

Actual Expenses

The table below provides information about actual account values and actual expenses. You may use the information in this table, together with the amount you invested, to estimate the expenses that you paid over the period. Simply divide your account value by $1,000 (for example, an $8,600 account value divided by $1,000 = 8.6), then multiply the result by the number in the table under the heading entitled "Actual Expenses Paid During Period" to estimate the expenses you paid on your account during this period.

Hypothetical Example for Comparison Purposes

The table below provides information about hypothetical account values and hypothetical expenses based on the Fund's actual expense ratio and an assumed rate of return of 5% per year before expenses, which is not the Fund's actual return. The hypothetical account values and expenses may not be used to estimate the actual ending account balance or expenses you paid for the period. You may use this information to compare the ongoing costs of investing in the Fund and other funds. To do so, compare this 5% hypothetical example with the 5% hypothetical examples that appear in the shareholder reports of the other funds.

Please note that the expenses shown in the table are meant to highlight your ongoing costs only and do not reflect any transactional costs, such as sales charges (loads, if applicable). Therefore, the information for each class in the table is useful in comparing ongoing costs only, and will not help you determine the relative total costs of owning different funds. In addition, if these transactional costs were included, your costs would have been higher.

	Beginning Account Value 9/30/20		Actual Ending Account Value 9/30/20		Hypothetical Ending Account Value		Actual Expenses Paid During Period*		Hypothetical Expenses Paid During Period*		Net Expense Ratio During Period**
Intermediate Municipal Income Portfolio Class I^	$	1,000.00	$	1,000.00	$	1,000.13	$	0.01	$	0.01		0.41	%
Intermediate Municipal Income Portfolio Class A^		1,000.00		1,000.00		1,000.11		0.02		0.02		0.80
Intermediate Municipal Income Portfolio Class C^		1,000.00		1,000.00		1,000.09		0.04		0.04		1.55
Intermediate Municipal Income Portfolio Class IS^		1,000.00		1,000.00		1,000.13		0.01		0.01		0.40

*  Expenses are calculated using each Fund Class' annualized net expense ratio (as disclosed), multiplied by the average account value over the period and multiplied by 1/366 (to reflect the actual days in the period).

**  Annualized.

^  The Fund commenced operations on September 30, 2020.

3

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Overview (unaudited)

Intermediate Municipal Income Portfolio

The Fund seeks to provide a high level of current income exempt from federal income tax, consistent with the preservation of capital.

Performance

The Fund's inception (September 30, 2020) was the same day as the close of the fiscal year on September 30, 2020.

Factors Affecting Performance

•  As of the end of the reporting period, the Fund did not have any performance history.

Management Strategies

•  The Fund invests in municipal securities, the income from which is exempt from federal income tax, using a combination of top-down and bottom-up research to determine duration and yield positioning, sector and credit quality allocation, and security selection. The Fund targets an average portfolio duration of +/- 3 years of the average duration of its benchmark, the Bloomberg Barclays Municipal Bond 1-15 Year Index.

4

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments

Intermediate Municipal Income Portfolio

	Face Amount (000)		Value (000)
Fixed Income Securities (22.2%)
Municipal Bonds (22.2%)
Arizona (1.1%)
Salt Verde Financial Corp. Senior Gas Revenue Bonds 2007-1 5.00%, 12/1/37	$	200	$	271
California (2.6%)
California Los Angeles International Airport Subordinate Revenue Bonds 2018 Series A (AMT)
5.00%, 5/15/28		250		318
State of California Various Purpose General Obligation Refunding Bonds
5.00%, 11/1/30		250		341
				659
Connecticut (1.0%)
Connecticut State General Obligation Bonds 2019 Series A
5.00%, 4/15/31		200		258
Florida (3.3%)
County of Miami-Dade Aviation Revenue Refunding Bonds Series 2016A
5.00%, 10/1/24		225		261
Jacksonville Special Revenue and Refunding Bonds, Series 2020A
5.00%, 10/1/26		250		314
School Board of Miami-Dade County (The) TANs, Series 2020
2.00%, 2/25/21		250		252
				827
Massachusetts (1.3%)
University of Massachusetts Building Authority Refunding Revenue Bonds Senior Series 2019-1
5.00%, 5/1/29		250		335
Nevada (1.4%)
Clark County School District Nevada General Obligation Building and Refunding Bonds Series 2017A
5.00%, 6/15/25		300		357
New York (3.8%)
City of New York General Obligation Bonds Fiscal 2018 Series C
5.00%, 8/1/29		250		316
Hudson Yards Infrastructure Corp. Second Indenture Revenue Bonds Fiscal 2017 Series A
5.00%, 2/15/31		250		301
New York City Transitional Finance Authority Future Tax Secured Revenue 2021 Series A
5.00%, 11/1/27		250		321
				938

	Face Amount (000)		Value (000)
Pennsylvania (1.4%)
Pennsylvania State General Obligation Bonds, First Series of 2020
5.00%, 5/1/31	$	250	$	337
South Carolina (1.0%)
South Carolina Transportation Infrastructure Bank Revenue Refunding Bonds, Series 2003B
1 Month USD LIBOR + 0.45%, 0.55%, 10/1/31 (a)		250		249
Texas (5.3%)
Austin Electric Utility System Revenue Series 2015A
5.00%, 11/15/25		250		309
Georgetown Independent School District Variable Rate Unlimited Tax School Building Bonds Series 2016-B
2.00%, 8/1/41		250		262
Harris County Cultural Education Facilities Finance Corp. Hospital Revenue Bonds Series 2014A
5.00%, 12/1/25		160		189
Love Field Airport Modernization Corp. General Airport Revenue Bonds, Series 2017 (AMT)
5.00%, 11/1/31		250		291
Pasadena Independent School District Variable Rate Unlimited Tax School Building Bonds, Series 2015B
1.50%, 2/15/44		260		272
				1,323
Total Fixed Income Securities (Cost $5,553)				5,554
Total Investments (22.2%) (Cost $5,553) (b)				5,554
Other Assets in Excess of Liabilities (77.8%)				19,446
Net Assets (100.0%)			$	25,000

(a)  Floating or variable rate securities: The rates disclosed are as of September 30, 2020. For securities based on a published reference rate and spread, the reference rate and spread are indicated in the description in the Portfolio of Investments. Certain variable rate securities may not be based on a published reference rate and spread but are determined by the issuer or agent and are based on current market conditions. These securities do not indicate a reference rate and spread in their description in the Portfolio of Investments.

(b)  At September 30, 2020, the aggregate cost for federal income tax purposes is approximately $5,553,000. The aggregate gross unrealized appreciation is approximately $8,000 and the aggregate gross unrealized depreciation is approximately $7,000, resulting in net unrealized appreciation of approximately $1,000.

AMT  Alternative Minimum Tax.

LIBOR  London Interbank Offered Rate.

TANs  Tax Anticipation Notes.

USD  United States Dollar

The accompanying notes are an integral part of the financial statements.
5

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Intermediate Municipal Income Portfolio

Summary of Investments by State

Classification	Percentage of Total Investments
Texas		23.8	%
New York		16.9
Florida		14.9
Other*		14.0
California		11.9
Nevada		6.4
Pennsylvania		6.1
Massachusetts		6.0
Total Investments		100.0	%

*  Industries and/or investment types representing less than 5% of total investments.

The accompanying notes are an integral part of the financial statements.
6

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Intermediate Municipal Income Portfolio

Statement of Assets and Liabilities	September 30, 2020 (000)
Assets:
Investments in Securities of Unaffiliated Issuers, at Value (Cost $5,553)	$	5,554
Cash		25,000
Prepaid Offering Costs		131
Due from Adviser		73
Interest Receivable		43
Total Assets		30,801
Liabilities:
Payable for Investments Purchased		5,596
Payable for Offering Costs		132
Payable for Professional Fees		67
Payable for Transfer Agency Fees — Class I		—	@
Payable for Transfer Agency Fees — Class A		—	@
Payable for Transfer Agency Fees — Class C		—	@
Payable for Shareholder Services Fees — Class A		—	@
Payable for Distribution and Shareholder Services Fees — Class C		—	@
Payable for Custodian Fees		—	@
Payable for Administration Fees		—	@
Other Liabilities		6
Total Liabilities		5,801
Net Assets	$	25,000
Net Assets Consist of:
Paid-in-Capital	$	25,000
Total Accumulated Loss		(—	@)
Net Assets	$	25,000
CLASS I:
Net Assets	$	24,970
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		2,497,000
Net Asset Value, Offering and Redemption Price Per Share	$	10.00
CLASS A:
Net Assets	$	10
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		1,000
Net Asset Value, Redemption Price Per Share	$	10.00
Maximum Sales Load		3.25	%
Maximum Sales Charge	$	0.34
Maximum Offering Price Per Share	$	10.34
CLASS C:
Net Assets	$	10
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		1,000
Net Asset Value, Offering and Redemption Price Per Share	$	10.00
CLASS IS:
Net Assets	$	10
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		1,000
Net Asset Value, Offering and Redemption Price Per Share	$	10.00

@  Amount is less than $500.

The accompanying notes are an integral part of the financial statements.
7

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Intermediate Municipal Income Portfolio

Statement of Operations	Period Ended September 30, 2020^ (000)
Expenses:
Professional Fees	$	67
Shareholder Reporting Fees		5
Transfer Agency Fees — Class I (Note E)		—	@
Transfer Agency Fees — Class A (Note E)		—	@
Transfer Agency Fees — Class C (Note E)		—	@
Transfer Agency Fees — Class IS (Note E)		—	@
Shareholder Services Fees — Class A (Note D)		—	@
Distribution and Shareholder Services Fees — Class C (Note D)		—	@
Advisory Fees (Note B)		—	@
Custodian Fees (Note F)		—	@
Administration Fees (Note C)		—	@
Pricing Fees		—	@
Offering Costs		—	@
Other Expenses		2
Total Expenses		74
Expenses Reimbursed by Adviser (Note B)		(73	)
Reimbursement of Class Specific Expenses — Class A (Note B)		(—	@)
Reimbursement of Class Specific Expenses — Class C (Note B)		(—	@)
Reimbursement of Class Specific Expenses — Class IS (Note B)		(—	@)
Waiver of Advisory Fees (Note B)		(—	@)
Net Expenses		1
Net Investment Loss		(1	)
Change in Unrealized Appreciation (Depreciation):
Investments		1
Net Decrease in Net Assets Resulting from Operations	$	(—	@)

^  Commencement of Operations.

@  Amount is less than $500.

The accompanying notes are an integral part of the financial statements.
8

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Intermediate Municipal Income Portfolio

Statement of Changes in Net Assets	Period Ended September 30, 2020^ (000)
Increase (Decrease) in Net Assets:
Operations:
Net Investment Loss	$	(1	)
Net Change in Unrealized Appreciation (Depreciation)		1
Net Decrease in Net Assets Resulting from Operations		(—	@)
Capital Share Transactions:(1)
Class I:
Subscribed		24,970
Class A:
Subscribed		10
Class C:
Subscribed		10
Class IS:
Subscribed		10
Net Increase in Net Assets Resulting from Capital Share Transactions		25,000
Total Increase in Net Assets		25,000
Net Assets:
Beginning of Period		—
End of Period	$	25,000
(1)   Capital Share Transactions:
Class I:
Shares Subscribed		2,497
Class A:
Shares Subscribed		1
Class C:
Shares Subscribed		1
Class IS:
Shares Subscribed		1

^  Commencement of Operations.

@  Amount is less than $500.

The accompanying notes are an integral part of the financial statements.
9

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Intermediate Municipal Income Portfolio

	Class I
Selected Per Share Data and Ratios	Period Ended September 30, 2020(1)
Net Asset Value, Beginning of Period	$	10.00
Loss from Investment Operations:
Net Investment Loss(2)		(0.00	)(3)
Net Realized and Unrealized Gain		0.00	(3)
Total from Investment Operations		(0.00	)(3)
Net Asset Value, End of Period	$	10.00
Total Return(4)		0.00	%(5)
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	24,970
Ratio of Expenses Before Expense Limitation		2.03	%(6)
Ratio of Expenses After Expense Limitation		0.41	%(6)
Ratio of Net Investment Loss		(0.41	)%(6)
Portfolio Turnover Rate		0	%(5)

(1)  Commencement of Operations.

(2)  Per share amount is based on average shares outstanding.

(3)  Amount is less than $0.005 per share.

(4)  Calculated based on the net asset value as of the last business day of the period.

(5)  Not annualized.

(6)  Annualized.

The accompanying notes are an integral part of the financial statements.
10

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Intermediate Municipal Income Portfolio

	Class A
Selected Per Share Data and Ratios	Period Ended September 30, 2020(1)
Net Asset Value, Beginning of Period	$	10.00
Loss from Investment Operations:
Net Investment Loss(2)		(0.00	)(3)
Net Realized and Unrealized Gain		0.00	(3)
Total from Investment Operations		(0.00	)(3)
Net Asset Value, End of Period	$	10.00
Total Return(4)		0.00	%(5)
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	10
Ratio of Expenses Before Expense Limitation		16.15	%(6)
Ratio of Expenses After Expense Limitation		0.80	%(6)
Ratio of Net Investment Loss		(0.80	)%(6)
Portfolio Turnover Rate		0	%(5)

(1)  Commencement of Operations.

(2)  Per share amount is based on average shares outstanding.

(3)  Amount is less than $0.005 per share.

(4)  Calculated based on the net asset value which does not reflect sales charges, if applicable, as of the last business day of the period.

(5)  Not annualized.

(6)  Annualized.

The accompanying notes are an integral part of the financial statements.
11

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Intermediate Municipal Income Portfolio

	Class C
Selected Per Share Data and Ratios	Period Ended September 30, 2020(1)
Net Asset Value, Beginning of Period	$	10.00
Loss from Investment Operations:
Net Investment Loss(2)		(0.00	)(3)
Net Realized and Unrealized Gain		0.00	(3)
Total from Investment Operations		(0.00	)(3)
Net Asset Value, End of Period	$	10.00
Total Return(4)		0.00	%(5)
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	10
Ratio of Expenses Before Expense Limitation		16.88	%(6)
Ratio of Expenses After Expense Limitation		1.55	%(6)
Ratio of Net Investment Loss		(1.55	)%(6)
Portfolio Turnover Rate		0	%(5)

(1)  Commencement of Operations.

(2)  Per share amount is based on average shares outstanding.

(3)  Amount is less than $0.005 per share.

(4)  Calculated based on the net asset value which does not reflect sales charges, if applicable, as of the last business day of the period.

(5)  Not annualized.

(6)  Annualized.

The accompanying notes are an integral part of the financial statements.
12

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Intermediate Municipal Income Portfolio

	Class IS
Selected Per Share Data and Ratios	Period Ended September 30, 2020(1)
Net Asset Value, Beginning of Period	$	10.00
Loss from Investment Operations:
Net Investment Loss(2)		(0.00	)(3)
Net Realized and Unrealized Gain		0.00	(3)
Total from Investment Operations		(0.00	)(3)
Net Asset Value, End of Period	$	10.00
Total Return(4)		0.00	%(5)
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	10
Ratio of Expenses Before Expense Limitation		15.89	%(6)
Ratio of Expenses After Expense Limitation		0.40	%(6)
Ratio of Net Investment Loss		(0.40	)%(6)
Portfolio Turnover Rate		0	%(5)

(1)  Commencement of Operations.

(2)  Per share amount is based on average shares outstanding.

(3)  Amount is less than $0.005 per share.

(4)  Calculated based on the net asset value as of the last business day of the period.

(5)  Not annualized.

(6)  Annualized.

The accompanying notes are an integral part of the financial statements.
13

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements

Morgan Stanley Institutional Fund Trust ("Trust'') is registered under the Investment Company Act of 1940, as amended (the "Act''), as an open-end management investment company. The Trust is comprised of twelve separate, active funds (individually referred to as a "Fund," collectively as the "Funds"). The Trust applies investment company accounting and reporting guidance. All Funds are considered diversified for purposes of the Act.

The accompanying financial statements relate to the Intermediate Municipal Income Portfolio. The Fund seeks to provide a high level of current income exempt from federal income tax, consistent with the preservation of capital.

The Fund commenced operations on September 30, 2020 and offers four classes of shares — Class I, Class A, Class C and Class IS.

A. Significant Accounting Policies: The following significant accounting policies are in conformity with U.S. generally accepted accounting principles ("GAAP"). Such policies are consistently followed by the Trust in the preparation of its financial statements. GAAP may require management to make estimates and assumptions that affect the reported amounts and disclosures in the financial statements. Actual results may differ from those estimates.

In March 2020, the Financial Accounting Standards Board ("FASB") issued an Accounting Standard Update, ASU 2020-04, Reference Rate Reform (Topic 848) — Facilitation of the Effects of Reference Rate Reform on Financial Reporting ("ASU 2020-04"), which provides optional, temporary relief with respect to the financial reporting of contracts subject to certain types of modifications due to the planned discontinuation of the London Interbank Offered Rate ("LIBOR") and other IBOR-based reference rates at the end of 2021. The temporary relief provided by ASU 2020-04 is effective for certain reference rate-related contract modifications that occur during the period from March 12, 2020 through December 31, 2022. Management is evaluating the impact of ASU 2020-04 on the Fund's investments, derivatives, debt and other contracts that will undergo reference rate-related modifications as a result of the reference rate reform.

In August 2018, FASB issued Accounting Standards Update ("ASU") 2018-13, Fair Value Measurement (Topic 820) — Disclosures Framework — Changes to Disclosure Requirements of Fair Value Measurement ("ASU 2018-13") which introduces new fair value disclosure requirements as well as eliminates and modifies certain existing fair value disclosure requirements. ASU 2018-13 would be effective for fiscal years

beginning after December 15, 2019 and for interim periods within those fiscal years; however, management has elected to early adopt ASU 2018-13 as permitted by the standard. The impact of the Fund's adoption was limited to changes in the Fund's financial statement disclosures regarding fair value, primarily those disclosures related to transfers between levels of the fair value hierarchy and disclosure of the range and weighted average used to develop significant unobservable inputs for Level 3 fair value measurements, when applicable.

1.  Security Valuation: (1) Certain portfolio securities may be valued by an outside pricing service/vendor approved by the Trust's Board of Trustees (the "Trustees"). The pricing service/vendor may employ a pricing model that takes into account, among other things, bids, yield spreads and/or other market data and specific security characteristics. Alternatively, if a valuation is not available from an outside pricing service/vendor, and the security trades on an exchange, the security may be valued at its latest reported sale price (or at the exchange official closing price if such exchange reports an official closing price), prior to the time when assets are valued. If there are no sales on a given day and if there is no official exchange closing price for that day, the security is valued at the mean between the last reported bid and asked prices if such bid and asked prices are available in the relevant exchanges. If only bid prices are available then the latest bid price may be used. If Morgan Stanley Investment Management Inc. (the "Adviser"), a wholly-owned subsidiary of Morgan Stanley, determines that the price provided by the outside pricing service/vendor or exchange does not reflect the security's fair value or is unable to provide a price, prices from brokers or dealers may also be utilized. In these circumstances, the value of the security will be the mean of bid and asked prices obtained from brokers or dealers; and (2) when market quotations are not readily available, including circumstances under which the Adviser determines that the closing price, last sale price or the mean between the last reported bid and asked prices are not reflective of a security's market value, portfolio securities are valued at their fair value as determined in good faith under procedures established by and under the general supervision of the Trustees. Occasionally, developments affecting the closing prices of securities and other assets may occur between the times at which valuations of such securities are determined (that is, close of the foreign market on which the securities trade) and the close of business of the New York Stock Exchange ("NYSE"). If

14

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

developments occur during such periods that are expected to materially affect the value of such securities, such valuations may be adjusted to reflect the estimated fair value of such securities as of the close of the NYSE, as determined in good faith by the Trustees or by the Adviser using a pricing service and/or procedures approved by the Trustees.

The Trustees have responsibility for determining in good faith the fair value of the investments, and the Trustees may appoint others, such as the Trust's Adviser or a valuation committee, to assist the Trustees in determining fair value and to make the actual calculations pursuant to the fair valuation methodologies previously approved by the Trustees. Under procedures approved by the Trustees, the Trust's Adviser has formed a Valuation Committee whose members are approved by the Trustees. The Valuation Committee provides administration and oversight of the Trust's valuation policies and procedures, which are reviewed at least annually by the Trustees. These procedures allow the Trust to utilize independent pricing services, quotations from securities and financial instrument dealers and other market sources to determine fair value.

2.  Fair Value Measurement: FASB Accounting Standards Codification^TM ("ASC") 820, "Fair Value Measurement" ("ASC 820"), defines fair value as the value that the Fund would receive to sell an investment or pay to transfer a liability in a timely transaction with an independent buyer in the principal market, or in the absence of a principal market, the most advantageous market for the investment or liability. ASC 820 establishes a three-tier hierarchy to distinguish between (1) inputs that reflect the assumptions market participants would use in valuing an asset or liability developed based on market data obtained from sources independent of the reporting entity (observable inputs) and (2) inputs that reflect the reporting entity's own assumptions about the assumptions market participants would use in valuing an asset or liability developed based on the best information available in the circumstances (unobservable inputs) and to establish classification of fair value measurements for disclosure purposes. Various inputs are used in determining the value of the Fund's investments. The inputs are summarized in the three broad levels listed below:

•  Level 1 – unadjusted quoted prices in active markets for identical investments

•  Level 2 – other significant observable inputs (including quoted prices for similar investments, interest rates, prepayment speeds, credit risk, etc.)

•  Level 3 – significant unobservable inputs including the Fund's own assumptions in determining the fair value of investments. Factors considered in making this determination may include, but are not limited to, information obtained by contacting the issuer, analysts, or the appropriate stock exchange (for exchange-traded securities), analysis of the issuer's financial statements or other available documents and, if necessary, available information concerning other securities in similar circumstances.

The inputs or methodology used for valuing securities are not necessarily an indication of the risk associated with investing in those securities and the determination of the significance of a particular input to the fair value measurement in its entirety requires judgment and considers factors specific to each security.

The following is a summary of the inputs used to value the Fund's investments as of September 30, 2020:

Investment Type	Level 1 Unadjusted quoted prices (000)		Level 2 Other significant observable inputs (000)		Level 3 Significant unobservable inputs (000)		Total (000)
Assets:
Fixed Income Securities
Municipal Bonds	$	—	$	5,554	$	—	$	5,554
Total Assets	$	—	$	5,554	$	—	$	5,554

Transfers between investment levels may occur as the markets fluctuate and/or the availability of data used in an investment's valuation changes.

3.  Indemnifications: The Trust enters into contracts that contain a variety of indemnifications. The Trust's maximum exposure under these arrangements is unknown. However, the Trust has not had prior claims or losses pursuant to these contracts and expects the risk of loss to be remote.

4.  Dividends and Distributions to Shareholders: Dividends and distributions to shareholders are recorded on the ex-dividend date. Dividends from net investment

15

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

income, if any, are declared and paid monthly. Net realized capital gains, if any, are distributed at least annually.

5.  Security Transactions, Income and Expenses: Security transactions are accounted for on the trade date (date the order to buy or sell is executed). Realized gains and losses on the sale of investment securities are determined on the specific identified cost method. Dividend income and other distributions are recorded on the ex-dividend date (except for certain foreign dividends which may be recorded as soon as the Fund is informed of such dividends) net of applicable withholding taxes. Interest income is recognized on the accrual basis except where collection is in doubt. Discounts are accreted and premiums are amortized over the life of the respective securities. Most expenses of the Trust can be directly attributed to a particular Fund. Expenses which cannot be directly attributed are apportioned among the Funds based upon relative net assets or other appropriate methods. Income, expenses (other than class specific expenses — distribution and shareholder services, transfer agency and sub transfer agency fees) and realized and unrealized gains or losses are allocated to each class of shares based upon their relative net assets.

B. Advisory Fees: The Adviser, a wholly-owned subsidiary of Morgan Stanley, provides the Fund with advisory services under the terms of an Investment Advisory Agreement, paid quarterly, at an annual rate of 0.35% of the average daily net assets of the Fund.

The Adviser has agreed to reduce its advisory fee and/or reimburse the Fund so that total annual Fund operating expenses, excluding certain investment related expenses, taxes, interest and other extraordinary expenses (including litigation), will not exceed 0.45% for Class I shares, 0.80% for Class A shares, 1.55% for Class C shares and 0.40% for Class IS shares. The fee waivers and/or expense reimbursements will continue for at least one year from the date of the Fund's prospectus or until such time as the Trustees act to discontinue all or a portion of such waivers and/or reimbursements when they deem such action is appropriate. The Adviser may make additional voluntary fee waivers and/or expense reimbursements and may discontinue these voluntary fee waivers and/or expense reimbursements at any time in the future. For the period ended September 30, 2020, less than $500 of advisory fees were waived and approximately $73,000 of other expenses were reimbursed by the Adviser pursuant to this arrangement.

C. Administration Fees: The Adviser also serves as Administrator to the Trust and provides administrative services pursuant to an Administration Agreement for an annual fee, accrued daily and paid monthly, of 0.08% of the Fund's average daily net assets. Under a Sub-Administration Agreement between the Administrator and State Street, State Street provides certain administrative services to the Trust. For such services, the Administrator pays State Street a portion of the fee the Administrator receives from the Fund.

D. Distribution and Shareholder Services Fees: Morgan Stanley Distribution, Inc. ("MSDI" or the "Distributor"), a wholly-owned subsidiary of the Adviser, and an indirect subsidiary of Morgan Stanley, serves as the Trust's Distributor of Fund shares pursuant to a Distribution Agreement. The Trust has adopted a Shareholder Services Plan with respect to Class A shares pursuant to Rule 12b-1 under the Act. Under the Shareholder Services Plan, the Fund pays the Distributor a shareholder services fee, accrued daily and paid monthly, at an annual rate of 0.25% of the Fund's average daily net assets attributable to Class A shares.

The Trust has adopted a Distribution and Shareholder Services Plan with respect to Class C shares pursuant to Rule 12b-1 under the Act. Under the Distribution and Shareholder Services Plan, the Fund pays the Distributor a distribution fee, accrued daily and paid monthly, at an annual rate of 0.75% and a shareholder services fee, accrued daily and paid monthly, at an annual rate of 0.25% of the Fund's average daily net assets attributable to Class C shares.

The distribution and shareholder services fees are used to support the expenses associated with servicing and maintaining accounts. The Distributor may compensate other parties for providing shareholder support services to investors who purchase Class A and Class C shares.

E. Dividend Disbursing and Transfer Agent: The Trust's dividend disbursing and transfer agent is DST Asset Manager Solutions, Inc. ("DST"). Pursuant to a Transfer Agency Agreement, the Trust pays DST a fee based on the number of classes, accounts and transactions relating to the Funds of the Trust.

F. Custodian Fees: State Street (the "Custodian") also serves as Custodian for the Trust in accordance with a Custodian Agreement. The Custodian holds cash, securities and other assets of the Trust as required by the Act. Custody fees are payable monthly based on assets held in custody, invest-

16

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

ment purchases and sales activity and account maintenance fees, plus reimbursement for certain out-of-pocket expenses.

G. Security Transactions and Transactions with Affiliates: For the period ended September 30, 2020, purchases and sales of investment securities for the Fund, other than long-term U.S. Government securities and short-term investments were approximately $5,553,000 and $0, respectively. There were no purchases and sales of long-term U.S. Government securities for the period ended September 30, 2020. For the period ended September 30, 2020, the Fund did not have any transactions in affiliated investments.

The Fund is permitted to purchase and sell securities ("cross-trade") from and to other Morgan Stanley funds as well as other funds and client accounts for which the Adviser or an affiliate of the Adviser serves as investment adviser, pursuant to procedures approved by the Trustees in compliance with Rule 17a-7 under the Act (the "Rule"). Each cross-trade is executed at the current market price in compliance with provisions of the Rule. For the period ended September 30, 2020, the Fund did not engage in any cross-trade transactions.

The Fund has an unfunded Deferred Compensation Plan (the "Compensation Plan"), which allows each independent Trustee to defer payment of all, or a portion, of the fees he or she receives for serving on the Board of Trustees. Each eligible Trustee generally may elect to have the deferred amounts credited with a return equal to the total return on one or more of the Morgan Stanley funds that are offered as investment options under the Compensation Plan. Appreciation/depreciation and distributions received from these investments are recorded with an offsetting increase/decrease in the deferred compensation obligation and do not affect the NAV of the Fund.

H. Federal Income Taxes: It is the Fund's intention to continue to qualify as a regulated investment company and distribute all of its taxable and tax-exempt income. Accordingly, no provision for federal income taxes is required in the financial statements.

The Fund may be subject to taxes imposed by countries in which it invests. Such taxes are generally based on income and/or capital gains earned or repatriated. Taxes are accrued based on net investment income, net realized gains and net unrealized appreciation as such income and/or gains are earned. Taxes may also be based on transactions in foreign currency and are accrued based on the value of investments denominated in such currency.

FASB ASC 740-10, "Income Taxes — Overall", sets forth a minimum threshold for financial statement recognition of the benefit of a tax position taken or expected to be taken in a tax return. Management has concluded there are no significant uncertain tax positions that would require recognition in the financial statements. If applicable, the Fund recognizes interest accrued related to unrecognized tax benefits in "Interest Expense" and penalties in "Other Expenses" in the Statement of Operations. The Fund files tax returns with the U.S. Internal Revenue Service, New York and various states. The tax period ended September 30, 2020, remains subject to examination by taxing authorities.

The tax character of distributions paid may differ from the character of distributions shown for GAAP purposes due to short-term capital gains being treated as ordinary income for tax purposes. There were no distributions paid during fiscal year 2020.

The amount and character of income and gains to be distributed are determined in accordance with income tax regulations which may differ from GAAP. These book/tax differences are either considered temporary or permanent in nature.

Temporary differences are attributable to differing book and tax treatments for the timing of the recognition of gains (losses) on certain investment transactions and the timing of the deductibility of certain expenses.

Permanent differences, due to a net operating loss, resulted in the following reclassifications among the components of net assets at September 30, 2020:

Total Accumulated Loss (000)			Paid-in-Capital (000)
$	—	@	$	(—	@)

@ Amount is less than $500.

At September 30, 2020, the Fund had no distributable earnings on a tax basis.

I. Other: At September 30, 2020, the Fund did not have record owners of 10% or greater.

J. Market Risk: Certain impacts to public health conditions particular to the coronavirus (COVID-19) outbreak could impact the operations and financial performance of certain of the Fund's investments. The extent of the impact to the financial performance of the Fund's investments will depend on future developments, including (i) the duration and spread of the outbreak, (ii) the restrictions and advisories, (iii) the effects on

17

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

the financial markets, and (iv) the effects on the economy overall, all of which are highly uncertain and cannot be predicted. If the financial performance of the Fund's investments is impacted because of these factors for an extended period, the Fund's investment results may be adversely affected.

K. LIBOR Risk: The Fund's investments, payment obligations and financing terms may be based on floating rates, such as London Interbank Offer Rate ("LIBOR"), Euro Interbank Offered Rate and other similar types of reference rates (each, a "Reference Rate"). These Reference Rates are generally intended to represent the rate at which contributing banks may obtain short-term borrowings from each other within certain financial markets. On July 27, 2017, the Chief Executive of the UK Financial Conduct Authority ("FCA"), which regulates LIBOR, announced that the FCA will no longer persuade nor require banks to submit rates for the calculation of LIBOR and certain other Reference Rates after 2021. Such announcement indicates that the continuation of LIBOR and other Reference Rates on the current basis cannot and will not be guaranteed after the end of 2021. This announcement and any additional regulatory or market changes may have an adverse impact on the Fund or its investments.

In advance of 2022, regulators and market participants are currently engaged in identifying successor Reference Rates ("Alternative Reference Rates"). Additionally, prior to the end of 2021, it is expected that market participants will focus on the transition mechanisms by which the Reference Rates in existing contracts or instruments may be amended, whether through marketwide protocols, fallback contractual provisions, bespoke negotiations or amendments or otherwise. Nonetheless, the termination of certain Reference Rates presents risks to the Fund. At this time, it is not possible to completely identify or predict the effect of any such changes, any establishment of Alternative Reference Rates or any other reforms to Reference Rates that may be enacted in the UK or elsewhere. The elimination of a Reference Rate or any other changes or reforms to the determination or supervision of Reference Rates could have an adverse impact on the market for or value of any securities or payments linked to those Reference Rates and other financial obligations held by the Fund or on its overall financial condition or results of operations.

18

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Report of Independent Registered Public Accounting Firm

To the Shareholders and Board of Trustees of
Morgan Stanley Institutional Fund Trust —
Intermediate Municipal Income Portfolio

Opinion on the Financial Statements

We have audited the accompanying statement of assets and liabilities of Intermediate Municipal Income Portfolio (the "Fund") (one of the funds constituting Morgan Stanley Institutional Fund Trust (the "Trust")), including the portfolio of investments, as of September 30, 2020, and the related statements of operations and changes in net assets and the financial highlights for the period from September 30, 2020 (commencement of operations) through September 30, 2020 and the related notes (collectively referred to as the "financial statements"). In our opinion, the financial statements present fairly, in all material respects, the financial position of Intermediate Municipal Income Portfolio (one of the funds constituting Morgan Stanley Institutional Fund Trust) at September 30, 2020, the results of its operations and the changes in its net assets and its financial highlights for the period from September 30, 2020 (commencement of operations) through September 30, 2020, in conformity with U.S. generally accepted accounting principles.

Basis for Opinion

These financial statements are the responsibility of the Trust's management. Our responsibility is to express an opinion on the Fund's financial statements based on our audit. We are a public accounting firm registered with the Public Company Accounting Oversight Board (United States) ("PCAOB") and are required to be independent with respect to the Trust in accordance with the U.S. federal securities law and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB.

We conducted our audit in accordance with the standards of the PCAOB. Those standards require that we plan and perform the audit to obtain reasonable assurance about whether the financial statements are free of material misstatement, whether due to error or fraud. The Trust is not required to have, nor were we engaged to perform, an audit of the Trust's internal control over financial reporting. As part of our audit, we are required to obtain an understanding of internal control over financial reporting, but not for the purpose of expressing an opinion on the effectiveness of the Trust's internal control over financial reporting. Accordingly, we express no such opinion.

Our audit included performing procedures to assess the risks of material misstatement of the financial statements, whether due to error or fraud, and performing procedures that respond to those risks. Such procedures included examining, on a test basis, evidence regarding the amounts and disclosures in the financial statements. Our procedures included confirmation of securities owned as of September 30, 2020 by correspondence with the custodian and brokers or by other appropriate auditing procedures where replies from brokers were not received. Our audit also included evaluating the accounting principles used and significant estimates made by management, as well as evaluating the overall presentation of the financial statements. We believe that our audit provides a reasonable basis for our opinion.

We have served as the auditor of one or more Morgan Stanley investment companies since 2000.
Boston, Massachusetts
November 24, 2020

19

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Advisory Agreement Approval (unaudited)

The Board considered the following factors at the time of approval of the contracts which occurred prior to commencement of operations.

Nature, Extent and Quality of Services

The Board reviewed and considered the nature and extent of the investment advisory services to be provided by the Adviser under the advisory agreement, including portfolio management, investment research and equity and fixed income securities trading. The Board also reviewed and considered the nature and extent of the non-advisory, administrative services to be provided by the Administrator under the administration agreement, including accounting, operations, clerical, bookkeeping, compliance, business management and planning, legal services and the provision of supplies, office space and utilities at the Adviser's expense. The Board also considered the Adviser's investment in personnel and infrastructure that benefits the Fund. (The Adviser and Administrator together are referred to as the "Adviser" and the advisory and administration agreements together are referred to as the "Management Agreement.") The Board also considered that the Adviser serves a variety of other investment advisory clients and has experience overseeing service providers.

The Board reviewed and considered the qualifications of the portfolio managers, the senior administrative managers and other key personnel of the Adviser who will provide the advisory and administrative services to the Fund. The Board determined that the Adviser's portfolio managers and key personnel are well qualified by education and/or training and experience to perform the services in an efficient and professional manner. The Board concluded that the nature and extent of the advisory and administrative services to be provided were necessary and appropriate for the conduct of the business and investment activities of the Fund and supported its decision to approve the Management Agreement.

Performance, Fees and Expenses of the Fund

The Board considered that the Adviser plans to arrange for a public offering of shares of the Fund to raise assets for investment and that the offering had not yet begun and concluded that, since the Fund currently had no assets to invest (other than seed capital required under the Investment Company Act) and had no track record of performance, this was not a factor it needed to address at the present time.

The Board reviewed the advisory and administrative fee rates (the "management fee rates") proposed to be paid by the Fund under the Management Agreement relative to comparable funds advised by the Adviser, when applicable, and compared to their peers as determined by the Adviser, and reviewed the anticipated total expense ratio of the Fund. The Board considered that the Fund requires the Adviser to develop processes, invest in additional resources and incur additional risks to successfully manage the Fund and concluded that the proposed management fee rate and anticipated total expense ratio would be competitive with its peer group averages.

Economies of Scale

The Board considered the growth prospects of the Fund and the structure of the proposed management fee schedule, which does not include breakpoints. The Board considered that the Fund's potential growth was uncertain and concluded that it would be premature to consider economies of scale as a factor in approving the Management Agreement at the present time.

Profitability of the Adviser and Affiliates

Since the Fund had not begun operations and had not paid any fees to the Adviser, the Board concluded that this was not a factor that needed to be considered at the present time.

Other Benefits of the Relationship

The Board considered other direct and indirect benefits to the Adviser and/or its affiliates to be derived from their relationship with the Fund and other funds advised by the Adviser. These benefits may include, among other things, fees for trading, distribution and/or shareholder servicing and for transaction processing and reporting platforms used by securities lending agents, and research received by the Adviser generated from commission dollars spent on funds' portfolio trading. Since the Fund had not begun operations and had not paid any fees to the Adviser, the Board concluded that these benefits were not a factor that needed to be considered at the present time.

20

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Advisory Agreement Approval (unaudited) (cont'd)

Resources of the Adviser and Historical Relationship Between the Fund and the Adviser

The Board considered whether the Adviser is financially sound and has the resources necessary to perform its obligations under the Management Agreement. The Board also reviewed and considered the organizational structure of the Adviser, the policies and procedures formulated and adopted by the Adviser for managing the Fund's operations and the Board's confidence in the competence and integrity of the senior managers and key personnel of the Adviser. The Board concluded that the Adviser has the financial resources necessary to fulfill its obligations under the Management Agreement and that it is beneficial for the Fund to enter into this relationship with the Adviser.

Other Factors and Current Trends

The Board considered the controls and procedures adopted and implemented by the Adviser and monitored by the Fund's Chief Compliance Officer and concluded that the conduct of business by the Adviser indicates a good faith effort on its part to adhere to high ethical standards in the conduct of the Fund's business.

As part of the Board's review, the Board received information from management on the impact of COVID-19 on the firm generally and the Adviser and the Fund in particular including, among other information, the pandemic's current and expected impact on the Fund's performance and operations.

General Conclusion

After considering and weighing all of the above factors, with various written materials and verbal information presented by the Adviser, the Board concluded that it would be in the best interest of the Fund and its future shareholders to approve the Management Agreement, which will remain in effect for two years and thereafter must be approved annually by the Board of the Fund if it is to continue in effect. In reaching this conclusion the Board did not give particular weight to any single piece of information or factor referenced above. It is possible that individual Board members may have weighed these factors, and the information presented, differently in reaching their individual decisions to approve the Management Agreement.

21

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Liquidity Risk Management Program (unaudited)

In compliance with Rule 22e-4 under the Investment Company Act of 1940, as amended (the "Liquidity Rule"), the Fund has adopted and implemented a liquidity risk management program (the "Program"), which is reasonably designed to assess and manage the risk that the Fund could not meet requests to redeem shares issued by the Fund without significant dilution of remaining investors' interests in the Fund (i.e., liquidity risk). The Fund's Board of Trustees (the "Board") previously approved the designation of the Liquidity Risk Subcommittee (the "LRS") as Program administrator. The LRS is comprised of representatives from various divisions within Morgan Stanley Investment Management.

At a meeting held on April 22-23, 2020, the Board reviewed a written report prepared by the LRS that addressed the Program's operation and assessed its adequacy, and effectiveness of implementation for the period from December 1, 2018, through December 31, 2019, as required under the Liquidity Rule. The report concluded that the Program operated effectively and was adequately and effectively implemented in all material aspects, and that the relevant controls and safeguards were appropriately designed to enable the LRS to administer the Program in compliance with the Liquidity Rule.

In accordance with the Program, the LRS assessed each Fund's liquidity risk no less frequently than annually taking into consideration certain factors, as applicable, such as (i) investment strategy and liquidity of portfolio investments, (ii) short-term and long-term cash flow projections and (iii) holdings of cash and cash equivalents and borrowing arrangements and other funding sources. Certain factors are considered under both normal and reasonably foreseeable stressed conditions.

Each Fund portfolio investment is classified into one of four liquidity categories, which classification is assessed at least monthly by the LRS. The classification is based on a determination of the number of days it is reasonably expected to take to convert the investment into cash, or sell or dispose of the investment, in current market conditions without significantly changing the market value of the investment. Liquidity classification determinations take into account various market, trading and investment-specific considerations, as well as market depth, and in some cases utilize third-party vendor data.

The Liquidity Rule limits a fund's investments in illiquid investments to 15% of its net assets and requires funds that do not primarily hold assets that are highly liquid investments to determine and maintain a minimum percentage of the fund's net assets to be invested in highly liquid investments (highly liquid investment minimum or "HLIM"). The LRS believes that the Program includes provisions reasonably designed to review, monitor and comply with the 15% limit on illiquid investments and for determining, periodically reviewing and complying with the HLIM requirement, as applicable.

There can be no assurance that the Program will achieve its objectives under all circumstances in the future. Please refer to the Fund's prospectus for more information regarding the Fund's exposure to liquidity risk and other risks to which it may be subject.

22

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Privacy Notice (unaudited)  April 2019

FACTS	WHAT DOES MSIM DO WITH YOUR PERSONAL INFORMATION?
Why?	Financial companies choose how they share your personal information. Federal law gives consumers the right to limit some but not all sharing. Federal law also requires us to tell you how we collect, share, and protect your personal information. Please read this notice carefully to understand what we do.
What?	The types of personal information we collect and share depend on the product or service you have with us. This information can include: n Social Security number and income n investment experience and risk tolerance n checking account number and wire transfer instructions
How?	All financial companies need to share customers' personal information to run their everyday business. In the section below, we list the reasons financial companies can share their customers' personal information; the reasons MSIM chooses to share; and whether you can limit this sharing.

Reasons we can share your personal information	Does MSIM share?	Can you limit this sharing?
For our everyday business purposes — such as to process your transactions, maintain your account(s), respond to court orders and legal investigations, or report to credit bureaus	Yes	No
For our marketing purposes — to offer our products and services to you	Yes	No
For joint marketing with other financial companies	No	We don't share
For our affiliates' everyday business purposes — information about your transactions and experiences	Yes	No
For our affiliates' everyday business purposes — information about your creditworthiness	No	We don't share
For our affiliates to market to you	No	We don't share
For non-affiliates to market to you	No	We don't share

Questions?Call toll-free (844) 312-6327 or email: imprivacyinquiries@morganstanley.com

23

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Privacy Notice (unaudited) (cont'd)  April 2019

Who we are

Who is providing this notice? Morgan Stanley Investment Management, Inc. and its affiliated registered investment advisers, registered broker-dealers, and registered and unregistered funds ("MSIM")

What we do

How does MSIM protect my personal information?	To protect your personal information from unauthorized access and use, we use security measures that comply with federal law. These measures include computer safeguards and secured files and buildings. We have policies governing the proper handling of customer information by personnel and requiring third parties that provide support to adhere to appropriate security standards with respect to such information.
How does MSIM collect my personal information?	We collect your personal information, for example, when you n open an account or make deposits or withdrawals from your account n buy securities from us or make a wire transfer n give us your contact information We also collect your personal information from others, such as credit bureaus, affiliates, or other companies.
Why can't I limit all sharing?	Federal law gives you the right to limit only n sharing for affiliates' everyday business purposes — information about your creditworthiness n affiliates from using your information to market to you n sharing for non-affiliates to market to you State laws and individual companies may give you additional rights to limit sharing. See below for more on your rights under state law.

Definitions

Affiliates	Companies related by common ownership or control. They can be financial and non-financial companies. n Our affiliates include companies with a Morgan Stanley name and financial companies such as Morgan Stanley Smith Barney LLC and Morgan Stanley & Co.
Non-affiliates	Companies not related by common ownership or control. They can be financial and non-financial companies. n MSIM does not share with non-affiliates so they can market to you.
Joint marketing	A formal agreement between non-affiliated financial companies that together market financial products or services to you. n MSIM doesn't jointly market

Other Important Information

Vermont: Except as permitted by law, we will not share personal information we collect about Vermont residents with Non-affiliates unless you provide us with your written consent to share such information.

California: Except as permitted by law, we will not share personal information we collect about California residents with Non-affiliates and we will limit sharing such personal information with our Affiliates to comply with California privacy laws that apply to us.

24

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited)

Independent Trustees:

Name, Address and Birth Year of Independent Trustee	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years and Other Relevant Professional Experience	Number of Funds in Fund Complex Overseen by Independent Trustee**	Other Directorships Held by Independent Trustee***
Frank L. Bowman c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1944	Trustee	Since August 2006	President, Strategic Decisions, LLC (consulting) (since February 2009); Director or Trustee of various Morgan Stanley Funds (since August 2006); Chairperson of the Compliance and Insurance Committee (since October 2015); formerly, Chairperson of the Insurance Sub-Committee of the Compliance and Insurance Committee (2007-2015); served as President and Chief Executive Officer of the Nuclear Energy Institute (policy organization) (February 2005-November 2008); retired as Admiral, U.S. Navy after serving over 38 years on active duty including 8 years as Director of the Naval Nuclear Propulsion Program in the Department of the Navy and the U.S. Department of Energy (1996-2004); served as Chief of Naval Personnel (July 1994-September 1996) and on the Joint Staff as Director of Political Military Affairs (June 1992-July 1994); knighted as Honorary Knight Commander of the Most Excellent Order of the British Empire; awarded the Officier de l'Orde National du Mérite by the French Government; elected to the National Academy of Engineering (2009).	86	Director of Naval and Nuclear Technologies LLP; Director Emeritus of the Armed Services YMCA; Member of the National Security Advisory Council of the Center for U.S. Global Engagement and a member of the CNA Military Advisory Board; Trustee of Fairhaven United Methodist Church; Member of the Board of Advisors of the Dolphin Scholarship Foundation; Director of other various non-profit organizations; Formerly, Director of BP p.l.c. (November 2010-May 2019).
Kathleen A. Dennis c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1953	Trustee	Since August 2006	President, Cedarwood Associates (mutual fund and investment management consulting) (since July 2006); Chairperson of the Liquidity and Alternatives Sub-Committee of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 2006); formerly, Senior Managing Director of Victory Capital Management (1993-2006).	86	Director of various non-profit organizations.
Nancy C. Everett c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1955	Trustee	Since January 2015	Chief Executive Officer, Virginia Commonwealth University Investment Company (since November 2015); Owner, OBIR, LLC (institutional investment management consulting) (since June 2014); formerly, Managing Director, BlackRock, Inc. (February 2011-December 2013); and Chief Executive Officer, General Motors Asset Management (a/k/a Promark Global Advisors, Inc.) (June 2005-May 2010).	87	Formerly, Member of Virginia Commonwealth University School of Business Foundation (2005-2016); Member of Virginia Commonwealth University Board of Visitors (2013-2015); Member of Committee on Directors for Emerging Markets Growth Fund, Inc. (2007-2010); Chairperson of Performance Equity Management, LLC (2006-2010); and Chairperson, GMAM Absolute Return Strategies Fund, LLC (2006-2010).

25

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Address and Birth Year of Independent Trustee	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years and Other Relevant Professional Experience	Number of Funds in Fund Complex Overseen by Independent Trustee**	Other Directorships Held by Independent Trustee***
Jakki L. Haussler c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1957	Trustee	Since January 2015	Chairman, Opus Capital Group (since January 1996); formerly, Chief Executive Officer, Opus Capital Group (1996-2019); Director, Capvest Venture Fund, LP (May 2000-December 2011); Partner, Adena Ventures, LP (July 1999-December 2010); Director, The Victory Funds (February 2005-July 2008).	87	Director of Service Corporation International and Member, Audit Committee and Investment Committee; Director of Cincinnati Bell Inc. and Member, Audit Committee and Governance and Nominating Committee; Director of Northern Kentucky University Foundation and Member, Investment Committee; Member of Chase College of Law Transactional Law Practice Center Board of Advisors; Director of Chase College of Law Board of Visitors; formerly, Member, University of Cincinnati Foundation Investment Committee; Member, Miami University Board of Visitors (2008-2011); Trustee of Victory Funds (2005-2008) and Chairman, Investment Committee (2007-2008); Member, Service Provider Committee (2005-2008) and Director of Best Transport (2006-2019).
Dr. Manuel H. Johnson c/o Johnson Smick International, Inc. 220 I Street, NE — Suite 200 Washington, D.C. 20002 Birth Year 1949	Trustee	Since July 1991	Senior Partner, Johnson Smick International, Inc. (consulting firm); Chairperson of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since July 1991); Co-Chairman and a founder of the Group of Seven Council (G7C) (international economic commission); formerly, Chairperson of the Audit Committee (July 1991-September 2006), Vice Chairman of the Board of Governors of the Federal Reserve System and Assistant Secretary of the U.S. Treasury.	86	Director of NVR, Inc. (home construction).
Joseph J. Kearns c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1942	Trustee	Since August 1994	Senior Adviser, Kearns & Associates LLC (investment consulting); Chairperson of the Audit Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 1994); Director, Rubicorn Investments (since February 2019); formerly, Deputy Chairperson of the Audit Committee (July 2003-September 2006) and Chairperson of the Audit Committee of various Morgan Stanley Funds (since August 1994); CFO of the J. Paul Getty Trust (1982-1999).	87	Prior to August 10, 2016, Director of Electro Rent Corporation (equipment leasing); Prior to December 31, 2013, Director of The Ford Family Foundation.

26

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Address and Birth Year of Independent Trustee	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years and Other Relevant Professional Experience	Number of Funds in Fund Complex Overseen by Independent Trustee**	Other Directorships Held by Independent Trustee***
Michael F. Klein c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1958	Trustee	Since August 2006	Managing Director, Aetos Alternatives Management, LP (since March 2000); Co-President, Aetos Alternatives Management, LP (since January 2004) and Co-Chief Executive Officer of Aetos Alternatives Management, LP (since August 2013); Chairperson of the Fixed Income Sub-Committee of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 2006); formerly, Managing Director, Morgan Stanley & Co. Inc. and Morgan Stanley Dean Witter Investment Management and President, various Morgan Stanley Funds (June 1998-March 2000); Principal, Morgan Stanley & Co. Inc. and Morgan Stanley Dean Witter Investment Management (August 1997-December 1999).	86	Director of certain investment funds managed or sponsored by Aetos Alternatives Management, LP; Director of Sanitized AG and Sanitized Marketing AG (specialty chemicals).
Patricia Maleski c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1960	Trustee	Since January 2017	Managing Director, JPMorgan Asset Management (2004-2016); Oversight and Control Head of Fiduciary and Conflicts of Interest Program (2015-2016); Chief Control Officer-Global Asset Management (2013-2015); President, JPMorgan Funds (2010-2013); Chief Administrative Officer (2004-2013); various other positions including Treasurer and Board Liaison (since 2001).	87	None.
W. Allen Reed c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1947	Chair of the Board and Trustee	Chair of the Boards since August 2020 and Trustee since August 2006	Chair of the Boards of various Morgan Stanley Funds (since August 2020); Chairperson of the Governance Committee; Chairperson of the Equity Sub-Committee of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 2006); formerly, Vice Chair of the Boards of various Morgan Stanley Funds (January 2020-August 2020); President and Chief Executive Officer of General Motors Asset Management; Chairman and Chief Executive Officer of the GM Trust Bank and Corporate Vice President of General Motors Corporation (August 1994-December 2005).	86	Formerly, Director of Legg Mason, Inc. (2006-2019); and Director of the Auburn University Foundation (2010-2015).

*  This is the earliest date the Trustee began serving the Morgan Stanley Funds. Each Trustee serves an indefinite term, until his or her successor is elected.

**  The Fund Complex includes (as of December 31, 2019) all open-end and closed-end funds (including all of their portfolios) advised by Morgan Stanley Investment Management Inc. (the "Adviser") and any funds that have an adviser that is an affiliated person of the Adviser (including, but not limited to, Morgan Stanley AIP GP LP).

***  This includes any directorships at public companies and registered investment companies held by the Trustee at any time during the past five years.

27

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited) (cont'd)

Executive Officers:

Name, Address and Birth Year of Executive Officer	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years
John H. Gernon 522 Fifth Avenue New York, NY 10036 Birth Year 1963	President and Principal Executive Officer	Since September 2013	President and Principal Executive Officer of the Equity and Fixed Income Funds and the Morgan Stanley AIP Funds (since September 2013) and the Liquidity Funds and various money market funds (since May 2014) in the Fund Complex; Managing Director of the Adviser; Head of Public Markets Product Development (since 2006).
Timothy J. Knierim 522 Fifth Avenue New York, NY 10036 Birth Year 1959	Chief Compliance Officer	Since December 2016	Managing Director of the Adviser and various entities affiliated with the Adviser; Chief Compliance Officer of various Morgan Stanley Funds and the Adviser (since December 2016) and Chief Compliance Officer of Morgan Stanley AIP GP LP (since 2014). Formerly, Managing Director and Deputy Chief Compliance Officer of the Adviser (2014-2016); and formerly, Chief Compliance Officer of Prudential Investment Management, Inc. (2007-2014).
Francis J. Smith 522 Fifth Avenue New York, NY 10036 Birth Year 1965	Treasurer and Principal Financial Officer	Treasurer since July 2003 and Principal Financial Officer since September 2002	Managing Director of the Adviser and various entities affiliated with the Adviser; Treasurer (since July 2003) and Principal Financial Officer of various Morgan Stanley Funds (since September 2002).
Mary E. Mullin 522 Fifth Avenue New York, NY 10036 Birth Year 1967	Secretary	Since June 1999	Managing Director of the Adviser; Secretary of various Morgan Stanley Funds (since June 1999).
Michael J. Key 522 Fifth Avenue New York, NY 10036 Birth Year 1979	Vice President	Since June 2017	Vice President of the Equity and Fixed Income Funds, Liquidity Funds, various money market funds and the Morgan Stanley AIP Funds in the Fund Complex (since June 2017); Executive Director of the Adviser; Head of Product Development for Equity and Fixed Income Funds (since August 2013).

*  This is the earliest date the officer began serving the Morgan Stanley Funds. Each officer serves a one-year term, until his or her successor is elected and qualifies.

28

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Adviser and Administrator

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

Distributor

Morgan Stanley Distribution, Inc.
522 Fifth Avenue
New York, New York 10036

Dividend Disbursing and Transfer Agent

DST Asset Manager Solutions, Inc.
2000 Crown Colony Drive
Quincy, Massachusetts 02169

Custodian

State Street Bank and Trust Company
One Lincoln Street
Boston, Massachusetts 02111

Legal Counsel

Dechert LLP
1095 Avenue of the Americas
New York, New York 10036

Counsel to the Independent Trustees

Perkins Coie LLP
1155 Avenue of the Americas,
22nd Floor
New York, New York 10036

Independent Registered Public Accounting Firm

Ernst & Young LLP
200 Clarendon Street
Boston, Massachusetts 02116

Reporting to Shareholders

Each Morgan Stanley fund provides a complete schedule of portfolio holdings in its Semi-Annual and the Annual Reports within 60 days of the end of the fund's second and fourth fiscal quarters. The Semi-Annual and Annual Reports are filed electronically with the Securities and Exchange Commission ("SEC") on Form N-CSRS and Form N-CSR, respectively. Morgan Stanley also delivers the Semi-Annual and Annual Reports to fund shareholders and makes these reports available on its public website, www.morganstanley.com/im/shareholderreports. Each Morgan Stanley non-money market fund also files a complete schedule of portfolio holdings with the SEC for the fund's first and third fiscal quarters as an attachment to Form N-PORT. Morgan Stanley does not deliver the reports for the first and third fiscal quarters to shareholders, nor are the reports posted to the Morgan Stanley public website. However, the holdings for each money market fund are posted to the Morgan Stanley public website. You may obtain the Form N-PORT filings (as well as the Form N-CSR and N-CSRS filings) by accessing the SEC's website, www.sec.gov. You can also request copies of these materials, upon payment of a duplicating fee, by electronic request at the SEC's email address (publicinfo@sec.gov).

Proxy Voting Policies and Procedures and Proxy Voting Record

You may obtain a copy of the Trust's Proxy Voting Policy and Procedures and information regarding how the Trust voted proxies relating to portfolio securities during the most recent twelve-month period ended June 30, without charge, upon request, by calling toll free 1 (800) 548-7786 or by visiting our website at www.morganstanley.com/im/shareholderreports. This information is also available on the SEC's website at www.sec.gov.

This report is authorized for distribution only when preceded or accompanied by a prospectus or summary prospectus of the applicable Fund of Morgan Stanley Institutional Fund Trust, which describes in detail the Fund's investment policies, risks, fees and expenses. Please read the prospectus carefully before you invest or send money. For additional information, including information regarding the investments comprising the Fund, please visit our website at www.morganstanley.com/im/shareholderreports or call toll free 1 (800) 548-7786.

29

Printed in U.S.A.
This Report has been prepared for shareholders and may be distributed to others only if preceded or accompanied by a current prospectus.

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

© 2020 Morgan Stanley. Morgan Stanley Distribution, Inc.

IFTIMIANN
3299188 EXP 11.30.21

INVESTMENT MANAGEMENT

Morgan Stanley Institutional Fund Trust

Municipal Income Portfolio

Annual Report

September 30, 2020

Beginning on January 1, 2021, as permitted by regulations adopted by the Securities and Exchange Commission ("SEC"), paper copies of the Fund's Annual and Semi-Annual Reports to Shareholders ("Shareholder Reports") will no longer be sent by mail, unless you specifically request paper copies of the Shareholder Reports from the Fund or from your financial intermediary, such as a broker-dealer or a bank. Instead, the Shareholder Reports will be made available on the Fund's website, https://www.morganstanley.com/im/shareholderreports and you will be notified by mail each time a Shareholder Report is posted and provided with a website link to access the Shareholder Report. If you already elected to receive Shareholder Reports electronically, you will not be affected by this change and you need not take any action. You may elect to receive Shareholder Reports and other communications from the Fund electronically anytime by contacting your financial intermediary or, if you are a direct investor, please follow the instructions on the envelope.

Beginning on January 1, 2019, you may elect to receive all future Shareholder Reports in paper free of charge. If you invest through a financial intermediary, you can contact your financial intermediary to request that you continue to receive paper copies of your Shareholder Reports. If you invest directly with the Fund, please follow the instructions on the envelope to let the Fund know you wish to continue receiving paper copies of your Shareholder Reports. Your election to receive Shareholder Reports in paper will apply to all funds held in your account if you invest through your financial intermediary or all funds held with the fund complex if you invest directly with a fund.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Table of Contents

Shareholders' Letter	2
Expense Example	3
Investment Overview	4
Portfolio of Investments	5
Statement of Assets and Liabilities	7
Statement of Operations	8
Statement of Changes in Net Assets	9
Financial Highlights	10
Notes to Financial Statements	14
Report of Independent Registered Public Accounting Firm	19
Investment Advisory Agreement Approval	20
Liquidity Risk Management Program	22
Privacy Notice	23
Trustee and Officer Information	25

This report is authorized for distribution only when preceded or accompanied by a prospectus or summary prospectus of the applicable Fund of the Morgan Stanley Institutional Fund Trust. To receive a prospectus and/or statement of additional information ("SAI"), which contains more complete information such as investment objectives, charges, expenses, policies for voting proxies, risk considerations and describes in detail each of the Fund's investment policies to the prospective investor, please call toll free 1 (800) 548-7786. Please read the prospectuses carefully before you invest or send money.

Additionally, you can access information about the Fund, including performance, characteristics and investment team commentary, through Morgan Stanley Investment Management's website: www.morganstanley.com/im/shareholderreports.

Market forecasts provided in this report may not necessarily come to pass. There is no guarantee that any sectors mentioned will continue to perform as discussed herein or that securities in such sectors will be held by the Fund in the future. There is no assurance that a fund will achieve its investment objective. Funds are subject to market risk, which is the possibility that market values of securities owned by the Fund will decline and, therefore, the value of the Fund's shares may be less than what you paid for them. Accordingly, you can lose money investing in this Fund. Please see the prospectus for more complete information on investment risks.

1

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Shareholders' Letter (unaudited)

Dear Shareholders,

We are pleased to provide this Annual Report, in which you will learn how your investment in Municipal Income Portfolio (the "Fund") performed during the period ended September 30, 2020 (when the Fund commenced operations).

Morgan Stanley Investment Management is a client-centric, investor-led organization. Our global presence, intellectual capital, and breadth of products and services enable us to partner with investors to meet the evolving challenges of today's financial markets. We aim to deliver superior investment service and to empower our clients to make the informed decisions that help them reach their investment goals.

As always, we thank you for selecting Morgan Stanley Investment Management, and look forward to working with you in the months and years ahead.

Sincerely,

John H. Gernon
President and Principal Executive Officer

October 2020

2

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Expense Example (unaudited)

Municipal Income Portfolio

As a shareholder of the Fund, you may incur two types of costs: (1) transactional costs, including sales charge (loads) on purchase payments; and (2) ongoing costs, which may include advisory fees, administration fees, distribution and shareholder services fees; and other Fund expenses. This example is intended to help you understand your ongoing costs (in dollars) of investing in the Fund and to compare these costs with the ongoing costs of investing in other mutual funds.

This example is based on an investment of $1,000 invested at the beginning of the period and held for the entire period 9/30/20-9/30/20.

Actual Expenses

The table below provides information about actual account values and actual expenses. You may use the information in this table, together with the amount you invested, to estimate the expenses that you paid over the period. Simply divide your account value by $1,000 (for example, an $8,600 account value divided by $1,000 = 8.6), then multiply the result by the number in the table under the heading entitled "Actual Expenses Paid During Period" to estimate the expenses you paid on your account during this period.

Hypothetical Example for Comparison Purposes

The table below provides information about hypothetical account values and hypothetical expenses based on the Fund's actual expense ratio and an assumed rate of return of 5% per year before expenses, which is not the Fund's actual return. The hypothetical account values and expenses may not be used to estimate the actual ending account balance or expenses you paid for the period. You may use this information to compare the ongoing costs of investing in the Fund and other funds. To do so, compare this 5% hypothetical example with the 5% hypothetical examples that appear in the shareholder reports of the other funds.

Please note that the expenses shown in the table are meant to highlight your ongoing costs only and do not reflect any transactional costs, such as sales charges (loads, if applicable). Therefore, the information for each class in the table is useful in comparing ongoing costs only, and will not help you determine the relative total costs of owning different funds. In addition, if these transactional costs were included, your costs would have been higher.

	Beginning Account Value 9/30/20		Actual Ending Account Value 9/30/20		Hypothetical Ending Account Value		Actual Expenses Paid During Period*		Hypothetical Expenses Paid During Period*		Net Expense Ratio During Period**
Municipal Income Portfolio Class I^	$	1,000.00	$	1,000.00	$	1,000.12	$	0.01	$	0.01		0.51	%
Municipal Income Portfolio Class A^		1,000.00		1,000.00		1,000.11		0.02		0.02		0.90
Municipal Income Portfolio Class C^		1,000.00		1,000.00		1,000.09		0.05		0.05		1.65
Municipal Income Portfolio Class IS^		1,000.00		1,000.00		1,000.12		0.01		0.01		0.50

*  Expenses are calculated using each Fund Class' annualized net expense ratio (as disclosed), multiplied by the average account value over the period and multiplied by 1/366 (to reflect the actual days in the period).

**  Annualized.

^  The Fund commenced operations on September 30, 2020.

3

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Overview (unaudited)

Municipal Income Portfolio

The Fund seeks to provide a high level of current income exempt from federal income tax, consistent with the preservation of capital.

Performance

The Fund's inception (September 30, 2020) was the same day as the close of the fiscal year on September 30, 2020.

Factors Affecting Performance

•  As of the end of the reporting period, the Fund did not have any performance history.

Management Strategies

•  The Fund invests in municipal securities, the income from which is exempt from federal income tax, using a combination of top-down and bottom-up research to determine duration and yield positioning, sector and credit quality allocation, and security selection. The Fund targets an average portfolio duration of +/- 3 years of the average duration of its benchmark, the Bloomberg Barclays Municipal Bond Index.

4

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments

Municipal Income Portfolio

	Face Amount (000)		Value (000)
Fixed Income Securities (18.8%)
Municipal Bonds (18.8%)
Arizona (1.1%)
Salt Verde Financial Corp. Senior Gas Revenue Bonds 2007-1 5.00%, 12/1/37	$	200	$	271
California (1.4%)
State of California Various Purpose General Obligation Refunding Bonds
5.00%, 11/1/30		250		341
Colorado (1.3%)
City of Colorado Springs Utilities System Revenue
5.00%, 11/15/50		250		327
Connecticut (1.0%)
Connecticut State General Obligation Bonds 2019 Series A
5.00%, 4/15/31		200		258
Florida (2.3%)
Jacksonville Special Revenue and Refunding Bonds Series 2020A
5.00%, 10/1/26		250		315
School Board of Miami-Dade County (The) TANs, Series 2020
2.00%, 2/25/21		250		252
				567
Massachusetts (1.3%)
University of Massachusetts Building Authority Refunding Revenue Bonds Senior Series 2019-1
5.00%, 5/1/29		250		335
New York (3.6%)
City of New York General Obligation Bonds Fiscal 2020 Series D
5.00%, 3/1/43		250		307
New York City Transitional Finance Authority Future Tax Secured Revenue 2021 Series C
4.00%, 5/1/44		250		289
Port Authority of New York & New Jersey Consolidated Bonds Two Hundred Twelfth Series
5.00%, 9/1/35		250		314
				910
Pennsylvania (1.4%)
Pennsylvania State General Obligation Bonds, First Series of 2020
5.00%, 5/1/31		250		336
South Carolina (1.0%)
South Carolina Transportation Infrastructure Bank Revenue Refunding Bonds, Series 2003B
1 Month USD LIBOR + 0.45%, 0.55%, 10/1/31 (a)		250		249

	Face Amount (000)		Value (000)
Texas (3.2%)
Georgetown Independent School District Variable Rate Unlimited Tax School Building Bonds, Series 2016-B
2.00%, 8/1/41	$	250	$	262
Love Field Airport Modernization Corp. General Airport Revenue Bonds, Series 2017 A (AMT)
5.00%, 11/1/31		250		291
Pasadena Independent School District Variable Rate Unlimited Tax School Building Bonds, Series 2015B
1.50%, 2/15/44		240		251
				804
Washington (1.2%)
King County Sewer Improvement and Refunding Revenue Bonds
4.00%, 1/1/46		250		293
Total Fixed Income Securities (Cost $4,696)				4,691
Total Investments (18.8%) (Cost $4,696) (b)				4,691
Other Assets in Excess of Liabilities (81.2%)				20,303
Net Assets (100.0%)			$	24,994

(a)  Floating or variable rate securities: The rates disclosed are as of September 30, 2020. For securities based on a published reference rate and spread, the reference rate and spread are indicated in the description in the Portfolio of Investments. Certain variable rate securities may not be based on a published reference rate and spread but are determined by the issuer or agent and are based on current market conditions. These securities do not indicate a reference rate and spread in their description in the Portfolio of Investments.

(b)  At September 30, 2020, the aggregate cost for federal income tax purposes is approximately $4,696,000. The aggregate gross unrealized appreciation is approximately $7,000 and the aggregate gross unrealized depreciation is approximately $12,000, resulting in net unrealized depreciation of approximately $5,000.

AMT  Alternative Minimum Tax.

LIBOR  London Interbank Offered Rate.

TANs  Tax Anticipation Notes.

USD  United States Dollar

The accompanying notes are an integral part of the financial statements.
5

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Municipal Income Portfolio

Summary of Investments by State

Classification	Percentage of Total Investments
New York		19.4	%
Texas		17.1
Florida		12.1
California		7.3
Pennsylvania		7.2
Massachusetts		7.1
Colorado		7.0
Washington		6.2
Arizona		5.8
Connecticut		5.5
South Carolina		5.3
Total Investments		100.0	%

The accompanying notes are an integral part of the financial statements.
6

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Municipal Income Portfolio

Statement of Assets and Liabilities	September 30, 2020 (000)
Assets:
Investments in Securities of Unaffiliated Issuers, at Value (Cost $4,696)	$	4,691
Cash		25,000
Prepaid Offering Costs		131
Due from Adviser		73
Interest Receivable		27
Total Assets		29,922
Liabilities:
Payable for Investments Purchased		4,723
Payable for Offering Costs		131
Payable for Professional Fees		67
Payable for Transfer Agency Fees — Class I		—	@
Payable for Transfer Agency Fees — Class A		—	@
Payable for Transfer Agency Fees — Class C		—	@
Payable for Shareholder Services Fees — Class A		—	@
Payable for Distribution and Shareholder Services Fees — Class C		—	@
Payable for Custodian Fees		—	@
Payable for Administration Fees		—	@
Other Liabilities		7
Total Liabilities		4,928
Net Assets	$	24,994
Net Assets Consist of:
Paid-in-Capital	$	25,000
Total Accumulated Loss		(6	)
Net Assets	$	24,994
CLASS I:
Net Assets	$	24,964
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		2,497,000
Net Asset Value, Offering and Redemption Price Per Share	$	10.00
CLASS A:
Net Assets	$	10
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		1,000
Net Asset Value, Redemption Price Per Share	$	10.00
Maximum Sales Load		3.25	%
Maximum Sales Charge	$	0.33
Maximum Offering Price Per Share	$	10.33
CLASS C:
Net Assets	$	10
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		1,000
Net Asset Value, Offering and Redemption Price Per Share	$	10.00
CLASS IS:
Net Assets	$	10
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		1,000
Net Asset Value, Offering and Redemption Price Per Share	$	10.00

@  Amount is less than $500.

The accompanying notes are an integral part of the financial statements.
7

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Municipal Income Portfolio

Statement of Operations	Period Ended September 30, 2020^ (000)
Expenses:
Professional Fees	$	67
Shareholder Reporting Fees		5
Transfer Agency Fees — Class I (Note E)		—	@
Transfer Agency Fees — Class A (Note E)		—	@
Transfer Agency Fees — Class C (Note E)		—	@
Transfer Agency Fees — Class IS (Note E)		—	@
Shareholder Services Fees — Class A (Note D)		—	@
Distribution and Shareholder Services Fees — Class C (Note D)		—	@
Advisory Fees (Note B)		—	@
Custodian Fees (Note F)		—	@
Administration Fees (Note C)		—	@
Pricing Fees		—	@
Offering Costs		—	@
Other Expenses		2
Total Expenses		74
Expenses Reimbursed by Adviser (Note B)		(73	)
Reimbursement of Class Specific Expenses — Class A (Note B)		(—	@)
Reimbursement of Class Specific Expenses — Class C (Note B)		(—	@)
Reimbursement of Class Specific Expenses — Class IS (Note B)		(—	@)
Waiver of Advisory Fees (Note B)		(—	@)
Net Expenses		1
Net Investment Loss		(1	)
Change in Unrealized Appreciation (Depreciation):
Investments		(5	)
Net Decrease in Net Assets Resulting from Operations	$	(6	)

^  Commencement of Operations.

@  Amount is less than $500.

The accompanying notes are an integral part of the financial statements.
8

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Municipal Income Portfolio

Statement of Changes in Net Assets	Period Ended September 30, 2020^ (000)
Increase (Decrease) in Net Assets:
Operations:
Net Investment Loss	$	(1	)
Net Change in Unrealized Appreciation (Depreciation)		(5	)
Net Decrease in Net Assets Resulting from Operations		(6	)
Capital Share Transactions:(1)
Class I:
Subscribed		24,970
Class A:
Subscribed		10
Class C:
Subscribed		10
Class IS:
Subscribed		10
Net Increase in Net Assets Resulting from Capital Share Transactions		25,000
Total Increase in Net Assets		24,994
Net Assets:
Beginning of Period		—
End of Period	$	24,994
(1)   Capital Share Transactions:
Class I:
Shares Subscribed		2,497
Class A:
Shares Subscribed		1
Class C:
Shares Subscribed		1
Class IS:
Shares Subscribed		1

^  Commencement of Operations.

The accompanying notes are an integral part of the financial statements.
9

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Municipal Income Portfolio

	Class I
Selected Per Share Data and Ratios	Period Ended September 30, 2020(1)
Net Asset Value, Beginning of Period	$	10.00
Loss from Investment Operations:
Net Investment Loss(2)		(0.00	)(3)
Net Realized and Unrealized Loss		(0.00	)(3)
Total from Investment Operations		(0.00	)(3)
Net Asset Value, End of Period	$	10.00
Total Return(4)		0.00	%(5)
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	24,964
Ratio of Expenses Before Expense Limitation		2.13	%(6)
Ratio of Expenses After Expense Limitation		0.51	%(6)
Ratio of Net Investment Loss		(0.51	)%(6)
Portfolio Turnover Rate		0	%(5)

(1)  Commencement of Operations.

(2)  Per share amount is based on average shares outstanding.

(3)  Amount is less than $0.005 per share.

(4)  Calculated based on the net asset value as of the last business day of the period.

(5)  Not annualized.

(6)  Annualized.

The accompanying notes are an integral part of the financial statements.
10

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Municipal Income Portfolio

	Class A
Selected Per Share Data and Ratios	Period Ended September 30, 2020(1)
Net Asset Value, Beginning of Period	$	10.00
Loss from Investment Operations:
Net Investment Loss(2)		(0.00	)(3)
Net Realized and Unrealized Loss		(0.00	)(3)
Total from Investment Operations		(0.00	)(3)
Net Asset Value, End of Period	$	10.00
Total Return(4)		0.00	%(5)
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	10
Ratio of Expenses Before Expense Limitation		16.22	%(6)
Ratio of Expenses After Expense Limitation		0.90	%(6)
Ratio of Net Investment Loss		(0.90	)%(6)
Portfolio Turnover Rate		0	%(5)

(1)  Commencement of Operations.

(2)  Per share amount is based on average shares outstanding.

(3)  Amount is less than $0.005 per share.

(4)  Calculated based on the net asset value which does not reflect sales charges, if applicable, as of the last business day of the period.

(5)  Not annualized.

(6)  Annualized.

The accompanying notes are an integral part of the financial statements.
11

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Municipal Income Portfolio

	Class C
Selected Per Share Data and Ratios	Period Ended September 30, 2020(1)
Net Asset Value, Beginning of Period	$	10.00
Loss from Investment Operations:
Net Investment Loss(2)		(0.00	)(3)
Net Realized and Unrealized Loss		(0.00	)(3)
Total from Investment Operations		(0.00	)(3)
Net Asset Value, End of Period	$	10.00
Total Return(4)		0.00	%(5)
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	10
Ratio of Expenses Before Expense Limitation		16.95	%(6)
Ratio of Expenses After Expense Limitation		1.65	%(6)
Ratio of Net Investment Loss		(1.65	)%(6)
Portfolio Turnover Rate		0	%(5)

(1)  Commencement of Operations.

(2)  Per share amount is based on average shares outstanding.

(3)  Amount is less than $0.005 per share.

(4)  Calculated based on the net asset value which does not reflect sales charges, if applicable, as of the last business day of the period.

(5)  Not annualized.

(6)  Annualized.

The accompanying notes are an integral part of the financial statements.
12

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Municipal Income Portfolio

	Class IS
Selected Per Share Data and Ratios	Period Ended September 30, 2020(1)
Net Asset Value, Beginning of Period	$	10.00
Loss from Investment Operations:
Net Investment Loss(2)		(0.00	)(3)
Net Realized and Unrealized Loss		(0.00	)(3)
Total from Investment Operations		(0.00	)(3)
Net Asset Value, End of Period	$	10.00
Total Return(4)		0.00	%(5)
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	10
Ratio of Expenses Before Expense Limitation		15.96	%(6)
Ratio of Expenses After Expense Limitation		0.50	%(6)
Ratio of Net Investment Loss		(0.50	)%(6)
Portfolio Turnover Rate		0	%(5)

(1)  Commencement of Operations.

(2)  Per share amount is based on average shares outstanding.

(3)  Amount is less than $0.005 per share.

(4)  Calculated based on the net asset value as of the last business day of the period.

(5)  Not annualized.

(6)  Annualized.

The accompanying notes are an integral part of the financial statements.
13

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements

Morgan Stanley Institutional Fund Trust ("Trust'') is registered under the Investment Company Act of 1940, as amended (the "Act"), as an open-end management investment company. The Trust is comprised of twelve separate, active funds (individually referred to as a "Fund," collectively as the "Funds"). The Trust applies investment company accounting and reporting guidance. All Funds are considered diversified for purposes of the Act.

The accompanying financial statements relate to the Municipal Income Portfolio. The Fund seeks to provide a high level of current income exempt from federal income tax, consistent with the preservation of capital.

The Fund commenced operations on September 30, 2020 and offers four classes of shares — Class I, Class A, Class C and Class IS.

A. Significant Accounting Policies: The following significant accounting policies are in conformity with U.S. generally accepted accounting principles ("GAAP"). Such policies are consistently followed by the Trust in the preparation of its financial statements. GAAP may require management to make estimates and assumptions that affect the reported amounts and disclosures in the financial statements. Actual results may differ from those estimates.

In March 2020, the Financial Accounting Standards Board ("FASB") issued an Accounting Standard Update, ASU 2020-04, Reference Rate Reform (Topic 848) — Facilitation of the Effects of Reference Rate Reform on Financial Reporting ("ASU 2020-04"), which provides optional, temporary relief with respect to the financial reporting of contracts subject to certain types of modifications due to the planned discontinuation of the London Interbank Offered Rate ("LIBOR") and other IBOR-based reference rates at the end of 2021. The temporary relief provided by ASU 2020-04 is effective for certain reference rate-related contract modifications that occur during the period from March 12, 2020 through December 31, 2022. Management is evaluating the impact of ASU 2020-04 on the Fund's investments, derivatives, debt and other contracts that will undergo reference rate-related modifications as a result of the reference rate reform.

In August 2018, FASB issued Accounting Standards Update ("ASU") 2018-13, Fair Value Measurement (Topic 820) — Disclosures Framework — Changes to Disclosure Requirements of Fair Value Measurement ("ASU 2018-13") which introduces new fair value disclosure requirements as well as

eliminates and modifies certain existing fair value disclosure requirements. ASU 2018-13 would be effective for fiscal years beginning after December 15, 2019 and for interim periods within those fiscal years; however, management has elected to early adopt ASU 2018-13 as permitted by the standard. The impact of the Fund's adoption was limited to changes in the Fund's financial statement disclosures regarding fair value, primarily those disclosures related to transfers between levels of the fair value hierarchy and disclosure of the range and weighted average used to develop significant unobservable inputs for Level 3 fair value measurements, when applicable.

1.  Security Valuation: (1) Certain portfolio securities may be valued by an outside pricing service/vendor approved by the Trust's Board of Trustees (the "Trustees"). The pricing service/vendor may employ a pricing model that takes into account, among other things, bids, yield spreads and/or other market data and specific security characteristics. Alternatively, if a valuation is not available from an outside pricing service/vendor, and the security trades on an exchange, the security may be valued at its latest reported sale price (or at the exchange official closing price if such exchange reports an official closing price), prior to the time when assets are valued. If there are no sales on a given day and if there is no official exchange closing price for that day, the security is valued at the mean between the last reported bid and asked prices if such bid and asked prices are available in the relevant exchanges. If only bid prices are available then the latest bid price may be used. If Morgan Stanley Investment Management Inc. (the "Adviser"), a wholly-owned subsidiary of Morgan Stanley, determines that the price provided by the outside pricing service/vendor or exchange does not reflect the security's fair value or is unable to provide a price, prices from brokers or dealers may also be utilized. In these circumstances, the value of the security will be the mean of bid and asked prices obtained from brokers or dealers; and (2) when market quotations are not readily available, including circumstances under which the Adviser determines that the closing price, last sale price or the mean between the last reported bid and asked prices are not reflective of a security's market value, portfolio securities are valued at their fair value as determined in good faith under procedures established by and under the general supervision of the Trustees. Occasionally, developments affecting the closing prices of securities and other assets may occur between the times at which valuations of such securities

14

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

are determined (that is, close of the foreign market on which the securities trade) and the close of business of the New York Stock Exchange ("NYSE"). If developments occur during such periods that are expected to materially affect the value of such securities, such valuations may be adjusted to reflect the estimated fair value of such securities as of the close of the NYSE, as determined in good faith by the Trustees or by the Adviser using a pricing service and/or procedures approved by the Trustees.

The Trustees have responsibility for determining in good faith the fair value of the investments, and the Trustees may appoint others, such as the Trust's Adviser or a valuation committee, to assist the Trustees in determining fair value and to make the actual calculations pursuant to the fair valuation methodologies previously approved by the Trustees. Under procedures approved by the Trustees, the Trust's Adviser has formed a Valuation Committee whose members are approved by the Trustees. The Valuation Committee provides administration and oversight of the Trust's valuation policies and procedures, which are reviewed at least annually by the Trustees. These procedures allow the Trust to utilize independent pricing services, quotations from securities and financial instrument dealers and other market sources to determine fair value.

2.  Fair Value Measurement: FASB Accounting Standards Codification^TM ("ASC") 820, "Fair Value Measurement" ("ASC 820"), defines fair value as the value that the Fund would receive to sell an investment or pay to transfer a liability in a timely transaction with an independent buyer in the principal market, or in the absence of a principal market, the most advantageous market for the investment or liability. ASC 820 establishes a three-tier hierarchy to distinguish between (1) inputs that reflect the assumptions market participants would use in valuing an asset or liability developed based on market data obtained from sources independent of the reporting entity (observable inputs) and (2) inputs that reflect the reporting entity's own assumptions about the assumptions market participants would use in valuing an asset or liability developed based on the best information available in the circumstances (unobservable inputs) and to establish classification of fair value measurements for disclosure purposes. Various inputs are used in determining the value

of the Fund's investments. The inputs are summarized in the three broad levels listed below:

•  Level 1 – unadjusted quoted prices in active markets for identical investments

•  Level 2 – other significant observable inputs (including quoted prices for similar investments, interest rates, prepayment speeds, credit risk, etc.)

•  Level 3 – significant unobservable inputs including the Fund's own assumptions in determining the fair value of investments. Factors considered in making this determination may include, but are not limited to, information obtained by contacting the issuer, analysts, or the appropriate stock exchange (for exchange-traded securities), analysis of the issuer's financial statements or other available documents and, if necessary, available information concerning other securities in similar circumstances.

The inputs or methodology used for valuing securities are not necessarily an indication of the risk associated with investing in those securities and the determination of the significance of a particular input to the fair value measurement in its entirety requires judgment and considers factors specific to each security.

The following is a summary of the inputs used to value the Fund's investments as of September 30, 2020:

Investment Type	Level 1 Unadjusted quoted prices (000)		Level 2 Other significant observable inputs (000)		Level 3 Significant unobservable inputs (000)		Total (000)
Assets:
Fixed Income Securities
Municipal Bonds	$	—	$	4,691	$	—	$	4,691
Total Assets	$	—	$	4,691	$	—	$	4,691

Transfers between investment levels may occur as the markets fluctuate and/or the availability of data used in an investment's valuation changes.

3.  Indemnifications: The Trust enters into contracts that contain a variety of indemnifications. The Trust's maximum exposure under these arrangements is unknown. However, the Trust has not had prior claims or losses pursuant to these contracts and expects the risk of loss to be remote.

15

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

4.  Dividends and Distributions to Shareholders: Dividends and distributions to shareholders are recorded on the ex-dividend date. Dividends from net investment income, if any, are declared and paid monthly. Net realized capital gains, if any, are distributed at least annually.

5.  Security Transactions, Income and Expenses: Security transactions are accounted for on the trade date (date the order to buy or sell is executed). Realized gains and losses on the sale of investment securities are determined on the specific identified cost method. Dividend income and other distributions are recorded on the ex-dividend date (except for certain foreign dividends which may be recorded as soon as the Fund is informed of such dividends) net of applicable withholding taxes. Interest income is recognized on the accrual basis except where collection is in doubt. Discounts are accreted and premiums are amortized over the life of the respective securities. Most expenses of the Trust can be directly attributed to a particular Fund. Expenses which cannot be directly attributed are apportioned among the Funds based upon relative net assets or other appropriate methods. Income, expenses (other than class specific expenses — distribution and shareholder services, transfer agency and sub transfer agency fees) and realized and unrealized gains or losses are allocated to each class of shares based upon their relative net assets.

B. Advisory Fees: The Adviser, a wholly-owned subsidiary of Morgan Stanley, provides the Fund with advisory services under the terms of an Investment Advisory Agreement, paid quarterly, at an annual rate of 0.45% of the average daily net assets of the Fund.

The Adviser has agreed to reduce its advisory fee and/or reimburse the Fund so that total annual Fund operating expenses, excluding certain investment related expenses, taxes, interest and other extraordinary expenses (including litigation), will not exceed 0.55% for Class I shares, 0.90% for Class A shares, 1.65% for Class C shares and 0.50% for Class IS shares. The fee waivers and/or expense reimbursements will continue for at least one year from the date of the Fund's prospectus or until such time as the Trustees act to discontinue all or a portion of such waivers and/or reimbursements when they deem such action is appropriate. The Adviser may make additional voluntary fee waivers and/or expense reimbursements and may discontinue these voluntary fee waivers and/or expense reimbursements at any time in the future. For the period ended September 30, 2020, less than $500 of advisory fees were

waived and approximately $73,000 of other expenses were reimbursed by the Adviser pursuant to this arrangement.

C. Administration Fees: The Adviser also serves as Administrator to the Trust and provides administrative services pursuant to an Administration Agreement for an annual fee, accrued daily and paid monthly, of 0.08% of the Fund's average daily net assets. Under a Sub-Administration Agreement between the Administrator and State Street, State Street provides certain administrative services to the Trust. For such services, the Administrator pays State Street a portion of the fee the Administrator receives from the Fund.

D. Distribution and Shareholder Services Fees: Morgan Stanley Distribution, Inc. ("MSDI" or the "Distributor"), a wholly-owned subsidiary of the Adviser, and an indirect subsidiary of Morgan Stanley, serves as the Trust's Distributor of Fund shares pursuant to a Distribution Agreement. The Trust has adopted a Shareholder Services Plan with respect to Class A shares pursuant to Rule 12b-1 under the Act. Under the Shareholder Services Plan, the Fund pays the Distributor a shareholder services fee, accrued daily and paid monthly, at an annual rate of 0.25% of the Fund's average daily net assets attributable to Class A shares.

The Trust has adopted a Distribution and Shareholder Services Plan with respect to Class C shares pursuant to Rule 12b-1 under the Act. Under the Distribution and Shareholder Services Plan, the Fund pays the Distributor a distribution fee, accrued daily and paid monthly, at an annual rate of 0.75% and a shareholder services fee, accrued daily and paid monthly, at an annual rate of 0.25% of the Fund's average daily net assets attributable to Class C shares.

The distribution and shareholder services fees are used to support the expenses associated with servicing and maintaining accounts. The Distributor may compensate other parties for providing shareholder support services to investors who purchase Class A and Class C shares.

E. Dividend Disbursing and Transfer Agent: The Trust's dividend disbursing and transfer agent is DST Asset Manager Solutions, Inc. ("DST"). Pursuant to a Transfer Agency Agreement, the Trust pays DST a fee based on the number of classes, accounts and transactions relating to the Funds of the Trust.

F. Custodian Fees: State Street (the "Custodian") also serves as Custodian for the Trust in accordance with a Custodian Agreement. The Custodian holds cash, securities and other assets of the Trust as required by the Act. Custody fees

16

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

are payable monthly based on assets held in custody, investment purchases and sales activity and account maintenance fees, plus reimbursement for certain out-of-pocket expenses.

G. Security Transactions and Transactions with Affiliates: For the period ended September 30, 2020, purchases and sales of investment securities for the Fund, other than long-term U.S. Government securities and short-term investments were approximately $4,696,000 and $0, respectively. There were no purchases and sales of long-term U.S. Government securities for the period ended September 30, 2020. For the period ended September 30, 2020, the Fund did not have any transactions in affiliated investments.

The Fund is permitted to purchase and sell securities ("cross-trade") from and to other Morgan Stanley funds as well as other funds and client accounts for which the Adviser or an affiliate of the Adviser serves as investment adviser, pursuant to procedures approved by the Trustees in compliance with Rule 17a-7 under the Act (the "Rule"). Each cross-trade is executed at the current market price in compliance with provisions of the Rule. For the period ended September 30, 2020, the Fund did not engage in any cross-trade transactions.

The Fund has an unfunded Deferred Compensation Plan (the "Compensation Plan"), which allows each independent Trustee to defer payment of all, or a portion, of the fees he or she receives for serving on the Board of Trustees. Each eligible Trustee generally may elect to have the deferred amounts credited with a return equal to the total return on one or more of the Morgan Stanley funds that are offered as investment options under the Compensation Plan. Appreciation/depreciation and distributions received from these investments are recorded with an offsetting increase/decrease in the deferred compensation obligation and do not affect the NAV of the Fund.

H. Federal Income Taxes: It is the Fund's intention to continue to qualify as a regulated investment company and distribute all of its taxable and tax-exempt income. Accordingly, no provision for federal income taxes is required in the financial statements.

The Fund may be subject to taxes imposed by countries in which it invests. Such taxes are generally based on income and/or capital gains earned or repatriated. Taxes are accrued based on net investment income, net realized gains and net unrealized appreciation as such income and/or gains are earned. Taxes may also be based on transactions in foreign currency and are accrued based on the value of investments denominated in such currency.

FASB ASC 740-10, "Income Taxes — Overall", sets forth a minimum threshold for financial statement recognition of the benefit of a tax position taken or expected to be taken in a tax return. Management has concluded there are no significant uncertain tax positions that would require recognition in the financial statements. If applicable, the Fund recognizes interest accrued related to unrecognized tax benefits in "Interest Expense" and penalties in "Other Expenses" in the Statement of Operations. The Fund files tax returns with the U.S. Internal Revenue Service, New York and various states. The tax period ended September 30, 2020, remains subject to examination by taxing authorities.

The tax character of distributions paid may differ from the character of distributions shown for GAAP purposes due to short-term capital gains being treated as ordinary income for tax purposes. There were no distributions paid during fiscal year 2020.

The amount and character of income and gains to be distributed are determined in accordance with income tax regulations which may differ from GAAP. These book/tax differences are either considered temporary or permanent in nature.

Temporary differences are attributable to differing book and tax treatments for the timing of the recognition of gains (losses) on certain investment transactions and the timing of the deductibility of certain expenses.

Permanent differences, due to a net operating loss, resulted in the following reclassifications among the components of net assets at September 30, 2020:

Total Accumulated Loss (000)			Paid-in- Capital (000)
$	—	@	$	(—	@)

@ Amount is less than $500.

At September 30, 2020, the Fund had no distributable earnings on a tax basis.

I. Other: At September 30, 2020, the Fund did not have record owners of 10% or greater.

J. Market Risk: Certain impacts to public health conditions particular to the coronavirus (COVID-19) outbreak could impact the operations and financial performance of certain of the Fund's investments. The extent of the impact to the financial performance of the Fund's investments will depend on future developments, including (i) the duration and spread of the outbreak, (ii) the restrictions and advisories, (iii) the effects on

17

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

the financial markets, and (iv) the effects on the economy overall, all of which are highly uncertain and cannot be predicted. If the financial performance of the Fund's investments is impacted because of these factors for an extended period, the Fund's investment results may be adversely affected.

K. LIBOR Risk. The Fund's investments, payment obligations and financing terms may be based on floating rates, such as London Interbank Offer Rate ("LIBOR"), Euro Interbank Offered Rate and other similar types of reference rates (each, a "Reference Rate"). These Reference Rates are generally intended to represent the rate at which contributing banks may obtain short-term borrowings from each other within certain financial markets. On July 27, 2017, the Chief Executive of the UK Financial Conduct Authority ("FCA"), which regulates LIBOR, announced that the FCA will no longer persuade nor require banks to submit rates for the calculation of LIBOR and certain other Reference Rates after 2021. Such announcement indicates that the continuation of LIBOR and other Reference Rates on the current basis cannot and will not be guaranteed after the end of 2021. This announcement and any additional regulatory or market changes may have an adverse impact on the Fund or its investments.

In advance of 2022, regulators and market participants are currently engaged in identifying successor Reference Rates ("Alternative Reference Rates"). Additionally, prior to the end of 2021, it is expected that market participants will focus on the transition mechanisms by which the Reference Rates in existing contracts or instruments may be amended, whether through marketwide protocols, fallback contractual provisions, bespoke negotiations or amendments or otherwise. Nonetheless, the termination of certain Reference Rates presents risks to the Fund. At this time, it is not possible to completely identify or predict the effect of any such changes, any establishment of Alternative Reference Rates or any other reforms to Reference Rates that may be enacted in the UK or elsewhere. The elimination of a Reference Rate or any other changes or reforms to the determination or supervision of Reference Rates could have an adverse impact on the market for or value of any securities or payments linked to those Reference Rates and other financial obligations held by the Fund or on its overall financial condition or results of operations.

18

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Report of Independent Registered Public Accounting Firm

To the Shareholders and Board of Trustees of
Morgan Stanley Institutional Fund Trust —
Municipal Income Portfolio

Opinion on the Financial Statements

We have audited the accompanying statement of assets and liabilities of Municipal Income Portfolio (the "Fund") (one of the funds constituting Morgan Stanley Institutional Fund Trust (the "Trust")), including the portfolio of investments, as of September 30, 2020, and the related statements of operations and changes in net assets and the financial highlights for the period from September 30, 2020 (commencement of operations) through September 30, 2020 and the related notes (collectively referred to as the "financial statements"). In our opinion, the financial statements present fairly, in all material respects, the financial position of Municipal Income Portfolio (one of the funds constituting Morgan Stanley Institutional Fund Trust) at September 30, 2020, the results of its operations and the changes in its net assets and its financial highlights for the period from September 30, 2020 (commencement of operations) through September 30, 2020, in conformity with U.S. generally accepted accounting principles.

Basis for Opinion

These financial statements are the responsibility of the Trust's management. Our responsibility is to express an opinion on the Fund's financial statements based on our audit. We are a public accounting firm registered with the Public Company Accounting Oversight Board (United States) ("PCAOB") and are required to be independent with respect to the Trust in accordance with the U.S. federal securities law and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB.

We conducted our audit in accordance with the standards of the PCAOB. Those standards require that we plan and perform the audit to obtain reasonable assurance about whether the financial statements are free of material misstatement, whether due to error or fraud. The Trust is not required to have, nor were we engaged to perform, an audit of the Trust's internal control over financial reporting. As part of our audit, we are required to obtain an understanding of internal control over financial reporting, but not for the purpose of expressing an opinion on the effectiveness of the Trust's internal control over financial reporting. Accordingly, we express no such opinion.

Our audit included performing procedures to assess the risks of material misstatement of the financial statements, whether due to error or fraud, and performing procedures that respond to those risks. Such procedures included examining, on a test basis, evidence regarding the amounts and disclosures in the financial statements. Our procedures included confirmation of securities owned as of September 30, 2020 by correspondence with the custodian and brokers or by other appropriate auditing procedures where replies from brokers were not received. Our audit also included evaluating the accounting principles used and significant estimates made by management, as well as evaluating the overall presentation of the financial statements. We believe that our audit provides a reasonable basis for our opinion.

We have served as the auditor of one or more Morgan Stanley investment companies since 2000.
Boston, Massachusetts
November 24, 2020

19

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Advisory Agreement Approval (unaudited)

The Board considered the following factors at the time of approval of the contracts which occurred prior to commencement of operations.

Nature, Extent and Quality of Services

The Board reviewed and considered the nature and extent of the investment advisory services to be provided by the Adviser under the advisory agreement, including portfolio management, investment research and equity and fixed income securities trading. The Board also reviewed and considered the nature and extent of the non-advisory, administrative services to be provided by the Administrator under the administration agreement, including accounting, operations, clerical, bookkeeping, compliance, business management and planning, legal services and the provision of supplies, office space and utilities at the Adviser's expense. The Board also considered the Adviser's investment in personnel and infrastructure that benefits the Fund. (The Adviser and Administrator together are referred to as the "Adviser" and the advisory and administration agreements together are referred to as the "Management Agreement.") The Board also considered that the Adviser serves a variety of other investment advisory clients and has experience overseeing service providers.

The Board reviewed and considered the qualifications of the portfolio managers, the senior administrative managers and other key personnel of the Adviser who will provide the advisory and administrative services to the Fund. The Board determined that the Adviser's portfolio managers and key personnel are well qualified by education and/or training and experience to perform the services in an efficient and professional manner. The Board concluded that the nature and extent of the advisory and administrative services to be provided were necessary and appropriate for the conduct of the business and investment activities of the Fund and supported its decision to approve the Management Agreement.

Performance, Fees and Expenses of the Fund

The Board considered that the Adviser plans to arrange for a public offering of shares of the Fund to raise assets for investment and that the offering had not yet begun and concluded that, since the Fund currently had no assets to invest (other than seed capital required under the Investment Company Act) and had no track record of performance, this was not a factor it needed to address at the present time.

The Board reviewed the advisory and administrative fee rates (the "management fee rates") proposed to be paid by the Fund under the Management Agreement relative to comparable funds advised by the Adviser, when applicable, and compared to their peers as determined by the Adviser, and reviewed the anticipated total expense ratio of the Fund. The Board considered that the Fund requires the Adviser to develop processes, invest in additional resources and incur additional risks to successfully manage the Fund and concluded that the proposed management fee rate and anticipated total expense ratio would be competitive with its peer group averages.

Economies of Scale

The Board considered the growth prospects of the Fund and the structure of the proposed management fee schedule, which does not include breakpoints. The Board considered that the Fund's potential growth was uncertain and concluded that it would be premature to consider economies of scale as a factor in approving the Management Agreement at the present time.

Profitability of the Adviser and Affiliates

Since the Fund had not begun operations and had not paid any fees to the Adviser, the Board concluded that this was not a factor that needed to be considered at the present time.

Other Benefits of the Relationship

The Board considered other direct and indirect benefits to the Adviser and/or its affiliates to be derived from their relationship with the Fund and other funds advised by the Adviser. These benefits may include, among other things, fees for trading, distribution and/or shareholder servicing and for transaction processing and reporting platforms used by securities lending agents, and research received by the Adviser generated from commission dollars spent on funds' portfolio trading. Since the Fund had not begun operations and had not paid any fees to the Adviser, the Board concluded that these benefits were not a factor that needed to be considered at the present time.

20

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Advisory Agreement Approval (unaudited) (cont'd)

Resources of the Adviser and Historical Relationship Between the Fund and the Adviser

The Board considered whether the Adviser is financially sound and has the resources necessary to perform its obligations under the Management Agreement. The Board also reviewed and considered the organizational structure of the Adviser, the policies and procedures formulated and adopted by the Adviser for managing the Fund's operations and the Board's confidence in the competence and integrity of the senior managers and key personnel of the Adviser. The Board concluded that the Adviser has the financial resources necessary to fulfill its obligations under the Management Agreement and that it is beneficial for the Fund to enter into this relationship with the Adviser.

Other Factors and Current Trends

The Board considered the controls and procedures adopted and implemented by the Adviser and monitored by the Fund's Chief Compliance Officer and concluded that the conduct of business by the Adviser indicates a good faith effort on its part to adhere to high ethical standards in the conduct of the Fund's business.

As part of the Board's review, the Board received information from management on the impact of COVID-19 on the firm generally and the Adviser and the Fund in particular including, among other information, the pandemic's current and expected impact on the Fund's performance and operations.

General Conclusion

After considering and weighing all of the above factors, with various written materials and verbal information presented by the Adviser, the Board concluded that it would be in the best interest of the Fund and its future shareholders to approve the Management Agreement, which will remain in effect for two years and thereafter must be approved annually by the Board of the Fund if it is to continue in effect. In reaching this conclusion the Board did not give particular weight to any single piece of information or factor referenced above. It is possible that individual Board members may have weighed these factors, and the information presented, differently in reaching their individual decisions to approve the Management Agreement.

21

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Liquidity Risk Management Program (unaudited)

In compliance with Rule 22e-4 under the Investment Company Act of 1940, as amended (the "Liquidity Rule"), the Fund has adopted and implemented a liquidity risk management program (the "Program"), which is reasonably designed to assess and manage the risk that the Fund could not meet requests to redeem shares issued by the Fund without significant dilution of remaining investors' interests in the Fund (i.e., liquidity risk). The Fund's Board of Trustees (the "Board") previously approved the designation of the Liquidity Risk Subcommittee (the "LRS") as Program administrator. The LRS is comprised of representatives from various divisions within Morgan Stanley Investment Management.

At a meeting held on April 22-23, 2020, the Board reviewed a written report prepared by the LRS that addressed the Program's operation and assessed its adequacy, and effectiveness of implementation for the period from December 1, 2018, through December 31, 2019, as required under the Liquidity Rule. The report concluded that the Program operated effectively and was adequately and effectively implemented in all material aspects, and that the relevant controls and safeguards were appropriately designed to enable the LRS to administer the Program in compliance with the Liquidity Rule.

In accordance with the Program, the LRS assessed each Fund's liquidity risk no less frequently than annually taking into consideration certain factors, as applicable, such as (i) investment strategy and liquidity of portfolio investments, (ii) short-term and long-term cash flow projections and (iii) holdings of cash and cash equivalents and borrowing arrangements and other funding sources. Certain factors are considered under both normal and reasonably foreseeable stressed conditions.

Each Fund portfolio investment is classified into one of four liquidity categories, which classification is assessed at least monthly by the LRS. The classification is based on a determination of the number of days it is reasonably expected to take to convert the investment into cash, or sell or dispose of the investment, in current market conditions without significantly changing the market value of the investment. Liquidity classification determinations take into account various market, trading and investment-specific considerations, as well as market depth, and in some cases utilize third-party vendor data.

The Liquidity Rule limits a fund's investments in illiquid investments to 15% of its net assets and requires funds that do not primarily hold assets that are highly liquid investments to determine and maintain a minimum percentage of the fund's net assets to be invested in highly liquid investments (highly liquid investment minimum or "HLIM"). The LRS believes that the Program includes provisions reasonably designed to review, monitor and comply with the 15% limit on illiquid investments and for determining, periodically reviewing and complying with the HLIM requirement, as applicable.

There can be no assurance that the Program will achieve its objectives under all circumstances in the future. Please refer to the Fund's prospectus for more information regarding the Fund's exposure to liquidity risk and other risks to which it may be subject.

22

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Privacy Notice (unaudited)  April 2019

FACTS	WHAT DOES MSIM DO WITH YOUR PERSONAL INFORMATION?
Why?	Financial companies choose how they share your personal information. Federal law gives consumers the right to limit some but not all sharing. Federal law also requires us to tell you how we collect, share, and protect your personal information. Please read this notice carefully to understand what we do.
What?	The types of personal information we collect and share depend on the product or service you have with us. This information can include: n Social Security number and income n investment experience and risk tolerance n checking account number and wire transfer instructions
How?	All financial companies need to share customers' personal information to run their everyday business. In the section below, we list the reasons financial companies can share their customers' personal information; the reasons MSIM chooses to share; and whether you can limit this sharing.

Reasons we can share your personal information	Does MSIM share?	Can you limit this sharing?
For our everyday business purposes — such as to process your transactions, maintain your account(s), respond to court orders and legal investigations, or report to credit bureaus	Yes	No
For our marketing purposes — to offer our products and services to you	Yes	No
For joint marketing with other financial companies	No	We don't share
For our affiliates' everyday business purposes — information about your transactions and experiences	Yes	No
For our affiliates' everyday business purposes — information about your creditworthiness	No	We don't share
For our affiliates to market to you	No	We don't share
For non-affiliates to market to you	No	We don't share

Questions?Call toll-free (844) 312-6327 or email: imprivacyinquiries@morganstanley.com

23

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Privacy Notice (unaudited) (cont'd)  April 2019

Who we are

Who is providing this notice? Morgan Stanley Investment Management, Inc. and its affiliated registered investment advisers, registered broker-dealers, and registered and unregistered funds ("MSIM")

What we do

How does MSIM protect my personal information?	To protect your personal information from unauthorized access and use, we use security measures that comply with federal law. These measures include computer safeguards and secured files and buildings. We have policies governing the proper handling of customer information by personnel and requiring third parties that provide support to adhere to appropriate security standards with respect to such information.
How does MSIM collect my personal information?	We collect your personal information, for example, when you n open an account or make deposits or withdrawals from your account n buy securities from us or make a wire transfer n give us your contact information We also collect your personal information from others, such as credit bureaus, affiliates, or other companies.
Why can't I limit all sharing?	Federal law gives you the right to limit only n sharing for affiliates' everyday business purposes — information about your creditworthiness n affiliates from using your information to market to you n sharing for non-affiliates to market to you State laws and individual companies may give you additional rights to limit sharing. See below for more on your rights under state law.

Definitions

Affiliates	Companies related by common ownership or control. They can be financial and non-financial companies. n Our affiliates include companies with a Morgan Stanley name and financial companies such as Morgan Stanley Smith Barney LLC and Morgan Stanley & Co.
Non-affiliates	Companies not related by common ownership or control. They can be financial and non-financial companies. n MSIM does not share with non-affiliates so they can market to you.
Joint marketing	A formal agreement between non-affiliated financial companies that together market financial products or services to you. n MSIM doesn't jointly market

Other Important Information

Vermont: Except as permitted by law, we will not share personal information we collect about Vermont residents with Non-affiliates unless you provide us with your written consent to share such information.

California: Except as permitted by law, we will not share personal information we collect about California residents with Non-affiliates and we will limit sharing such personal information with our Affiliates to comply with California privacy laws that apply to us.

24

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited)

Independent Trustees:

Name, Address and Birth Year of Independent Trustee	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years and Other Relevant Professional Experience	Number of Funds in Fund Complex Overseen by Independent Trustee**	Other Directorships Held by Independent Trustee***
Frank L. Bowman c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1944	Trustee	Since August 2006	President, Strategic Decisions, LLC (consulting) (since February 2009); Director or Trustee of various Morgan Stanley Funds (since August 2006); Chairperson of the Compliance and Insurance Committee (since October 2015); formerly, Chairperson of the Insurance Sub-Committee of the Compliance and Insurance Committee (2007-2015); served as President and Chief Executive Officer of the Nuclear Energy Institute (policy organization) (February 2005-November 2008); retired as Admiral, U.S. Navy after serving over 38 years on active duty including 8 years as Director of the Naval Nuclear Propulsion Program in the Department of the Navy and the U.S. Department of Energy (1996-2004); served as Chief of Naval Personnel (July 1994-September 1996) and on the Joint Staff as Director of Political Military Affairs (June 1992-July 1994); knighted as Honorary Knight Commander of the Most Excellent Order of the British Empire; awarded the Officier de l'Orde National du Mérite by the French Government; elected to the National Academy of Engineering (2009).	86	Director of Naval and Nuclear Technologies LLP; Director Emeritus of the Armed Services YMCA; Member of the National Security Advisory Council of the Center for U.S. Global Engagement and a member of the CNA Military Advisory Board; Trustee of Fairhaven United Methodist Church; Member of the Board of Advisors of the Dolphin Scholarship Foundation; Director of other various non-profit organizations; Formerly, Director of BP p.l.c. (November 2010-May 2019).
Kathleen A. Dennis c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1953	Trustee	Since August 2006	President, Cedarwood Associates (mutual fund and investment management consulting) (since July 2006); Chairperson of the Liquidity and Alternatives Sub-Committee of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 2006); formerly, Senior Managing Director of Victory Capital Management (1993-2006).	86	Director of various non-profit organizations.
Nancy C. Everett c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1955	Trustee	Since January 2015	Chief Executive Officer, Virginia Commonwealth University Investment Company (since November 2015); Owner, OBIR, LLC (institutional investment management consulting) (since June 2014); formerly, Managing Director, BlackRock, Inc. (February 2011-December 2013); and Chief Executive Officer, General Motors Asset Management (a/k/a Promark Global Advisors, Inc.) (June 2005-May 2010).	87	Formerly, Member of Virginia Commonwealth University School of Business Foundation (2005-2016); Member of Virginia Commonwealth University Board of Visitors (2013-2015); Member of Committee on Directors for Emerging Markets Growth Fund, Inc. (2007-2010); Chairperson of Performance Equity Management, LLC (2006-2010); and Chairperson, GMAM Absolute Return Strategies Fund, LLC (2006-2010).

25

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Address and Birth Year of Independent Trustee	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years and Other Relevant Professional Experience	Number of Funds in Fund Complex Overseen by Independent Trustee**	Other Directorships Held by Independent Trustee***
Jakki L. Haussler c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1957	Trustee	Since January 2015	Chairman, Opus Capital Group (since January 1996); formerly, Chief Executive Officer, Opus Capital Group (1996-2019); Director, Capvest Venture Fund, LP (May 2000-December 2011); Partner, Adena Ventures, LP (July 1999-December 2010); Director, The Victory Funds (February 2005-July 2008).	87	Director of Service Corporation International and Member, Audit Committee and Investment Committee; Director of Cincinnati Bell Inc. and Member, Audit Committee and Governance and Nominating Committee; Director of Northern Kentucky University Foundation and Member, Investment Committee; Member of Chase College of Law Transactional Law Practice Center Board of Advisors; Director of Chase College of Law Board of Visitors; formerly, Member, University of Cincinnati Foundation Investment Committee; Member, Miami University Board of Visitors (2008-2011); Trustee of Victory Funds (2005-2008) and Chairman, Investment Committee (2007-2008); Member, Service Provider Committee (2005-2008) and Director of Best Transport (2006-2019).
Dr. Manuel H. Johnson c/o Johnson Smick International, Inc. 220 I Street, NE — Suite 200 Washington, D.C. 20002 Birth Year 1949	Trustee	Since July 1991	Senior Partner, Johnson Smick International, Inc. (consulting firm); Chairperson of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since July 1991); Co-Chairman and a founder of the Group of Seven Council (G7C) (international economic commission); formerly, Chairperson of the Audit Committee (July 1991-September 2006), Vice Chairman of the Board of Governors of the Federal Reserve System and Assistant Secretary of the U.S. Treasury.	86	Director of NVR, Inc. (home construction).
Joseph J. Kearns c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1942	Trustee	Since August 1994	Senior Adviser, Kearns & Associates LLC (investment consulting); Chairperson of the Audit Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 1994); Director, Rubicorn Investments (since February 2019); formerly, Deputy Chairperson of the Audit Committee (July 2003-September 2006) and Chairperson of the Audit Committee of various Morgan Stanley Funds (since August 1994); CFO of the J. Paul Getty Trust (1982-1999).	87	Prior to August 10, 2016, Director of Electro Rent Corporation (equipment leasing); Prior to December 31, 2013, Director of The Ford Family Foundation.

26

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Address and Birth Year of Independent Trustee	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years and Other Relevant Professional Experience	Number of Funds in Fund Complex Overseen by Independent Trustee**	Other Directorships Held by Independent Trustee***
Michael F. Klein c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1958	Trustee	Since August 2006	Managing Director, Aetos Alternatives Management, LP (since March 2000); Co-President, Aetos Alternatives Management, LP (since January 2004) and Co-Chief Executive Officer of Aetos Alternatives Management, LP (since August 2013); Chairperson of the Fixed Income Sub-Committee of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 2006); formerly, Managing Director, Morgan Stanley & Co. Inc. and Morgan Stanley Dean Witter Investment Management and President, various Morgan Stanley Funds (June 1998-March 2000); Principal, Morgan Stanley & Co. Inc. and Morgan Stanley Dean Witter Investment Management (August 1997-December 1999).	86	Director of certain investment funds managed or sponsored by Aetos Alternatives Management, LP; Director of Sanitized AG and Sanitized Marketing AG (specialty chemicals).
Patricia Maleski c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1960	Trustee	Since January 2017	Managing Director, JPMorgan Asset Management (2004-2016); Oversight and Control Head of Fiduciary and Conflicts of Interest Program (2015-2016); Chief Control Officer-Global Asset Management (2013-2015); President, JPMorgan Funds (2010-2013); Chief Administrative Officer (2004-2013); various other positions including Treasurer and Board Liaison (since 2001).	87	None.
W. Allen Reed c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1947	Chair of the Board and Trustee	Chair of the Boards since August 2020 and Trustee since August 2006	Chair of the Boards of various Morgan Stanley Funds (since August 2020); Chairperson of the Governance Committee; Chairperson of the Equity Sub-Committee of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 2006); formerly, Vice Chair of the Boards of various Morgan Stanley Funds (January 2020-August 2020); President and Chief Executive Officer of General Motors Asset Management; Chairman and Chief Executive Officer of the GM Trust Bank and Corporate Vice President of General Motors Corporation (August 1994-December 2005).	86	Formerly, Director of Legg Mason, Inc. (2006-2019); and Director of the Auburn University Foundation (2010-2015).

*  This is the earliest date the Trustee began serving the Morgan Stanley Funds. Each Trustee serves an indefinite term, until his or her successor is elected.

**  The Fund Complex includes (as of December 31, 2019) all open-end and closed-end funds (including all of their portfolios) advised by Morgan Stanley Investment Management Inc. (the "Adviser") and any funds that have an adviser that is an affiliated person of the Adviser (including, but not limited to, Morgan Stanley AIP GP LP).

***  This includes any directorships at public companies and registered investment companies held by the Trustee at any time during the past five years.

27

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited) (cont'd)

Executive Officers:

Name, Address and Birth Year of Executive Officer	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years
John H. Gernon 522 Fifth Avenue New York, NY 10036 Birth Year 1963	President and Principal Executive Officer	Since September 2013	President and Principal Executive Officer of the Equity and Fixed Income Funds and the Morgan Stanley AIP Funds (since September 2013) and the Liquidity Funds and various money market funds (since May 2014) in the Fund Complex; Managing Director of the Adviser; Head of Public Markets Product Development (since 2006).
Timothy J. Knierim 522 Fifth Avenue New York, NY 10036 Birth Year 1959	Chief Compliance Officer	Since December 2016	Managing Director of the Adviser and various entities affiliated with the Adviser; Chief Compliance Officer of various Morgan Stanley Funds and the Adviser (since December 2016) and Chief Compliance Officer of Morgan Stanley AIP GP LP (since 2014). Formerly, Managing Director and Deputy Chief Compliance Officer of the Adviser (2014-2016); and formerly, Chief Compliance Officer of Prudential Investment Management, Inc. (2007-2014).
Francis J. Smith 522 Fifth Avenue New York, NY 10036 Birth Year 1965	Treasurer and Principal Financial Officer	Treasurer since July 2003 and Principal Financial Officer since September 2002	Managing Director of the Adviser and various entities affiliated with the Adviser; Treasurer (since July 2003) and Principal Financial Officer of various Morgan Stanley Funds (since September 2002).
Mary E. Mullin 522 Fifth Avenue New York, NY 10036 Birth Year 1967	Secretary	Since June 1999	Managing Director of the Adviser; Secretary of various Morgan Stanley Funds (since June 1999).
Michael J. Key 522 Fifth Avenue New York, NY 10036 Birth Year 1979	Vice President	Since June 2017	Vice President of the Equity and Fixed Income Funds, Liquidity Funds, various money market funds and the Morgan Stanley AIP Funds in the Fund Complex (since June 2017); Executive Director of the Adviser; Head of Product Development for Equity and Fixed Income Funds (since August 2013).

*  This is the earliest date the officer began serving the Morgan Stanley Funds. Each officer serves a one-year term, until his or her successor is elected and qualifies.

28

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Adviser and Administrator

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

Distributor

Morgan Stanley Distribution, Inc.
522 Fifth Avenue
New York, New York 10036

Dividend Disbursing and Transfer Agent

DST Asset Manager Solutions, Inc.
2000 Crown Colony Drive
Quincy, Massachusetts 02169

Custodian

State Street Bank and Trust Company
One Lincoln Street
Boston, Massachusetts 02111

Legal Counsel

Dechert LLP
1095 Avenue of the Americas
New York, New York 10036

Counsel to the Independent Trustees

Perkins Coie LLP
1155 Avenue of the Americas,
22nd Floor
New York, New York 10036

Independent Registered Public Accounting Firm

Ernst & Young LLP
200 Clarendon Street
Boston, Massachusetts 02116

Reporting to Shareholders

Each Morgan Stanley fund provides a complete schedule of portfolio holdings in its Semi-Annual and the Annual Reports within 60 days of the end of the fund's second and fourth fiscal quarters. The Semi-Annual and Annual Reports are filed electronically with the Securities and Exchange Commission ("SEC") on Form N-CSRS and Form N-CSR, respectively. Morgan Stanley also delivers the Semi-Annual and Annual Reports to fund shareholders and makes these reports available on its public website, www.morganstanley.com/im/shareholderreports. Each Morgan Stanley non-money market fund also files a complete schedule of portfolio holdings with the SEC for the fund's first and third fiscal quarters as an attachment to Form N-PORT. Morgan Stanley does not deliver the reports for the first and third fiscal quarters to shareholders, nor are the reports posted to the Morgan Stanley public website. However, the holdings for each money market fund are posted to the Morgan Stanley public website. You may obtain the Form N-PORT filings (as well as the Form N-CSR and N-CSRS filings) by accessing the SEC's website, www.sec.gov. You can also request copies of these materials, upon payment of a duplicating fee, by electronic request at the SEC's email address (publicinfo@sec.gov).

Proxy Voting Policies and Procedures and Proxy Voting Record

You may obtain a copy of the Trust's Proxy Voting Policy and Procedures and information regarding how the Trust voted proxies relating to portfolio securities during the most recent twelve-month period ended June 30, without charge, upon request, by calling toll free 1 (800) 548-7786 or by visiting our website at www.morganstanley.com/im/shareholderreports. This information is also available on the SEC's website at www.sec.gov.

This report is authorized for distribution only when preceded or accompanied by a prospectus or summary prospectus of the applicable fund of Morgan Stanley Institutional Fund Trust, which describes in detail the fund's investment policies, risks, fees and expenses. Please read the prospectus carefully before you invest or send money. For additional information, including information regarding the investments comprising the Fund, please visit our website at www.morganstanley.com/im/shareholderreports or call toll free 1 (800) 548-7786.

29

Printed in U.S.A.
This Report has been prepared for shareholders and may be distributed to others only if preceded or accompanied by a current prospectus.

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

© 2020 Morgan Stanley. Morgan Stanley Distribution, Inc.

IFTMIANN
3300494 EXP 11.30.21

INVESTMENT MANAGEMENT

Morgan Stanley Institutional Fund Trust

Senior Loan Portfolio

Annual Report

September 30, 2020

Beginning on January 1, 2021, as permitted by regulations adopted by the Securities and Exchange Commission ("SEC"), paper copies of the Fund's Annual and Semi-Annual Reports to Shareholders ("Shareholder Reports") will no longer be sent by mail, unless you specifically request paper copies of the Shareholder Reports from the Fund or from your financial intermediary, such as a broker-dealer or a bank. Instead, the Shareholder Reports will be made available on the Fund's website, https://www.morganstanley.com/im/shareholderreports and you will be notified by mail each time a Shareholder Report is posted and provided with a website link to access the Shareholder Report. If you already elected to receive Shareholder Reports electronically, you will not be affected by this change and you need not take any action. You may elect to receive Shareholder Reports and other communications from the Fund electronically anytime by contacting your financial intermediary or, if you are a direct investor, please follow the instructions on the envelope.

Beginning on January 1, 2019, you may elect to receive all future Shareholder Reports in paper free of charge. If you invest through a financial intermediary, you can contact your financial intermediary to request that you continue to receive paper copies of your Shareholder Reports. If you invest directly with the Fund, please follow the instructions on the envelope to let the Fund know you wish to continue receiving paper copies of your Shareholder Reports. Your election to receive Shareholder Reports in paper will apply to all funds held in your account if you invest through your financial intermediary or all funds held with the fund complex if you invest directly with a fund.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Table of Contents

Shareholders' Letter	2
Expense Example	3
Investment Overview	4
Portfolio of Investments	6
Statement of Assets and Liabilities	12
Statement of Operations	13
Statement of Changes in Net Assets	14
Financial Highlights	15
Notes to Financial Statements	19
Report of Independent Registered Public Accounting Firm	25
Investment Advisory Agreement Approval	26
Liquidity Risk Management Program	28
Privacy Notice	29
Trustee and Officer Information	31

This report is authorized for distribution only when preceded or accompanied by a prospectus or summary prospectus of the applicable Fund of the Morgan Stanley Institutional Fund Trust. To receive a prospectus and/or statement of additional information ("SAI"), which contains more complete information such as investment objectives, charges, expenses, policies for voting proxies, risk considerations and describes in detail each of the Fund's investment policies to the prospective investor, please call toll free 1 (800) 548-7786. Please read the prospectuses carefully before you invest or send money.

Additionally, you can access information about the Fund, including performance, characteristics and investment team commentary, through Morgan Stanley Investment Management's website: www.morganstanley.com/im/shareholderreports.

Market forecasts provided in this report may not necessarily come to pass. There is no guarantee that any sectors mentioned will continue to perform as discussed herein or that securities in such sectors will be held by the Fund in the future. There is no assurance that a fund will achieve its investment objective. Funds are subject to market risk, which is the possibility that market values of securities owned by the Fund will decline and, therefore, the value of the Fund's shares may be less than what you paid for them. Accordingly, you can lose money investing in this Fund. Please see the prospectus for more complete information on investment risks.

1

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Shareholders' Letter (unaudited)

Dear Shareholders,

We are pleased to provide this Annual Report, in which you will learn how your investment in Senior Loan Portfolio (the "Fund") performed during the period beginning January 31, 2020 (when the Fund commenced operations) and ended September 30, 2020.

Morgan Stanley Investment Management is a client-centric, investor-led organization. Our global presence, intellectual capital, and breadth of products and services enable us to partner with investors to meet the evolving challenges of today's financial markets. We aim to deliver superior investment service and to empower our clients to make the informed decisions that help them reach their investment goals.

As always, we thank you for selecting Morgan Stanley Investment Management, and look forward to working with you in the months and years ahead.

Sincerely,

John H. Gernon
President and Principal Executive Officer

October 2020

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Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Expense Example (unaudited)

Senior Loan Portfolio

As a shareholder of the Fund, you may incur two types of costs: (1) transactional costs, including sales charge (loads) on purchase payments; and (2) ongoing costs, which may include advisory fees, administration fees, distribution and shareholder services fees; and other Fund expenses. This example is intended to help you understand your ongoing costs (in dollars) of investing in the Fund and to compare these costs with the ongoing costs of investing in other mutual funds.

This example is based on an investment of $1,000 invested at the beginning of the six-month period ended September 30, 2020 and held for the entire six-month period.

Actual Expenses

The table below provides information about actual account values and actual expenses. You may use the information in this table, together with the amount you invested, to estimate the expenses that you paid over the period. Simply divide your account value by $1,000 (for example, an $8,600 account value divided by $1,000 = 8.6), then multiply the result by the number in the table under the heading entitled "Actual Expenses Paid During Period" to estimate the expenses you paid on your account during this period.

Hypothetical Example for Comparison Purposes

The table below provides information about hypothetical account values and hypothetical expenses based on the Fund's actual expense ratio and an assumed rate of return of 5% per year before expenses, which is not the Fund's actual return. The hypothetical account values and expenses may not be used to estimate the actual ending account balance or expenses you paid for the period. You may use this information to compare the ongoing costs of investing in the Fund and other funds. To do so, compare this 5% hypothetical example with the 5% hypothetical examples that appear in the shareholder reports of the other funds.

Please note that the expenses shown in the table are meant to highlight your ongoing costs only and do not reflect any transactional costs, such as sales charges (loads, if applicable). Therefore, the information for each class in the table is useful in comparing ongoing costs only, and will not help you determine the relative total costs of owning different funds. In addition, if these transactional costs were included, your costs would have been higher.

	Beginning Account Value 4/1/20		Actual Ending Account Value 9/30/20		Hypothetical Ending Account Value		Actual Expenses Paid During Period*		Hypothetical Expenses Paid During Period*		Net Expense Ratio During Period**
Senior Loan Portfolio Class I	$	1,000.00	$	1,121.70	$	1,021.25	$	3.98	$	3.79		0.75	%
Senior Loan Portfolio Class A		1,000.00		1,119.40		1,019.30		6.04		5.76		1.14
Senior Loan Portfolio Class C		1,000.00		1,114.10		1,015.50		10.04		9.57		1.90
Senior Loan Portfolio Class IS		1,000.00		1,121.70		1,021.25		3.98		3.79		0.75

*  Expenses are calculated using each Fund Class' annualized net expense ratio (as disclosed), multiplied by the average account value over the period and multiplied by 183/366 (to reflect the most recent one-half year period).

**  Annualized.

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Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Overview (unaudited)

Senior Loan Portfolio

The Fund seeks a high level of current income.

Performance

For the period from Fund inception on January 31, 2020 through September 30, 2020, the Fund's Class I shares had a total return based on net asset value and reinvestment of distributions per share of –1.84%, net of fees. The Fund's Class I shares underperformed against the Fund's benchmark, the S&P/LSTA Leveraged Loan Index (the "Index"), which returned –1.21%.

Factors Affecting Performance

•  As of the end of the reporting period, the Fund had less than one year of performance history. Such a short time frame would not provide a meaningful performance analysis as short-term returns may not be indicative of the Fund's long-term performance potential.

Management Strategies

•  The Fund aims to provide a high level of current income by investing in senior secured floating rate loans and other fixed income securities. To help achieve its objective, the investment team starts with a top-down macroeconomic assessment combined with rigorous bottom-up credit analysis.

•  Given the current market environment, the Fund has been overweight higher quality BB credits. This defensive posture helped contribute to outperformance during the beginning of 2020, but as the market recovered, we saw spreads in the riskier part of the market compress and perform well, leading the Fund to underperform.

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Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Overview (unaudited) (cont'd)

Senior Loan Portfolio

*  Minimum Investment

**  Commenced operations on January 31, 2020.

In accordance with SEC regulations, the Fund's performance shown assumes that all recurring fees (including management fees) were deducted and all dividends and distributions were reinvested. The performance of Class A, Class C and Class IS shares will vary from the performance of Class I shares and will be negatively impacted by additional fees assessed to those classes (where applicable).

Performance Compared to the S&P/LSTA Leveraged Loan Index⁽¹⁾ and the Lipper Loan Participation Funds Index⁽²⁾

	Period Ended September 30, 2020 Total Returns(3)
	One Year		Five Years		Ten Years		Since Inception(5)
Fund — Class I Shares w/o sales charges(4)		—		—		—		–1.84	%
Fund — Class A Shares w/o sales charges(4)		—		—		—		–2.07
Fund — Class A Shares with maximum 3.25% sales charges(4)		—		—		—		–5.29
Fund — Class C Shares w/o sales charges(4)		—		—		—		–2.59
Fund — Class C Shares with maximum 1.00% deferred sales charges(4)		—		—		—		–3.56
Fund — Class IS Shares w/o sales charges(4)		—		—		—		–1.84
S&P/LSTA Leveraged Loan Index		—		—		—		–1.21
Lipper Loan Participation Funds Index		—		—		—		–3.08

Performance data quoted represents past performance, which is no guarantee of future results, and current performance may be lower or higher than the figures shown. Performance assumes that all dividends and distributions, if any, were reinvested. Returns for period less than one year are not annualized. For the most recent month-end performance figures, please visit www.morganstanley.com/im/shareholderreports. Investment returns and principal value will fluctuate so that Fund shares, when redeemed, may be worth more or less than their original cost. Total returns do not reflect the deduction of taxes that a shareholder would pay on Fund distributions or the redemption of Fund shares. Performance of share classes will vary due to differences in sales charges and expenses.

⁽¹⁾  The S&P/LSTA (Standard & Poor's/Loan Syndications and Trading Association) Leveraged Loan Index is an index that covers more than 1,100 loan facilities and reflects the market-value-weighted performance of U.S. dollar denominated institutional leveraged loans. The Index is unmanaged and its returns do not include any sales charges or fees. Such costs would lower performance. It is not possible to invest directly in an index.

⁽²⁾  The Lipper Loan Participation Funds Index is an equally weighted performance index of the largest qualifying funds (based on net assets) in the Lipper Loan Participation Funds classification. The Index, which is adjusted for capital gains distributions and income dividends, is unmanaged and should not be considered an investment. There are currently 30 funds represented in this Index. As of the date of this report, the Fund was in the Lipper Loan Participation Funds classification.

⁽³⁾  Total returns for the Fund reflect expenses waived and/or reimbursed, if applicable, by the Adviser. Without such waivers and/or reimbursements, total returns would have been lower.

⁽⁴⁾  Commenced operations on January 31, 2020.

⁽⁵⁾  For comparative purposes, average annual since inception returns listed for the Indexes refer to the inception date of the Fund, not the inception of the Indexes.

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Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments

Senior Loan Portfolio

	Face Amount (000)		Value (000)
Fixed Income Securities (100.0%)
Corporate Bonds (17.2%)
Communications (3.7%)
Altice France SA 7.38%, 5/1/26 (a)	$	250	$	262
Avaya, Inc. 6.13%, 9/15/28 (a)		250		256
CSC Holdings LLC 5.50%, 4/15/27 (a)		250		263
iHeartCommunications, Inc. 4.75%, 1/15/28 (a)		500		472
LCPR Senior Secured Financing DAC 6.75%, 10/15/27 (a)		250		262
MDC Partners, Inc. 6.50%, 5/1/24 (a)		350		320
				1,835
Consumer, Cyclical (5.1%)
At Home Holding III, Inc. 8.75%, 9/1/25 (a)		500		523
Boyne USA, Inc. 7.25%, 5/1/25 (a)		225		237
Delta Air Lines, Inc./SkyMiles IP Ltd. 4.75%, 10/20/28 (a)		250		260
Downstream Development Authority of the Quapaw Tribe of Oklahoma 10.50%, 2/15/23 (a)		175		161
New Home Co., Inc. (The) 7.25%, 4/1/22		250		249
Rite Aid Corp. 7.50%, 7/1/25 (a)		250		247
Spirit Loyalty Cayman Ltd./Spirit IP Cayman Ltd. 8.00%, 9/20/25 (a)		100		106
Station Casinos LLC 4.50%, 2/15/28 (a)		500		461
Sugarhouse HSP Gaming Prop Mezz LP/ Sugarhouse HSP Gaming Finance Corp. 5.88%, 5/15/25 (a)		250		245
				2,489
Consumer, Non-Cyclical (2.2%)
Air Medical Group Holdings, Inc. 6.38%, 5/15/23 (a)		350		351
Simmons Foods, Inc. 5.75%, 11/1/24 (a)		250		251
Sotheby's 7.38%, 10/15/27 (a)		500		501
				1,103
Energy (0.4%)
Global Partners LP/GLP Finance Corp. 7.00%, 8/1/27		175		179
Finance (1.0%)
iStar, Inc. 4.75%, 10/1/24		250		242
Oxford Finance LLC/Oxford Finance Co-Issuer II, Inc. 6.38%, 12/15/22 (a)		250		245
				487

	Face Amount (000)		Value (000)
Industrials (4.3%)
Bombardier, Inc. 6.13%, 1/15/23 (a)	$	200	$	171
Builders FirstSource, Inc. 6.75%, 6/1/27 (a)		100		107
Cleaver-Brooks, Inc. 7.88%, 3/1/23 (a)		150		145
Grinding Media, Inc./Moly-Cop AltaSteel Ltd. 7.38%, 12/15/23 (a)		225		228
Kratos Defense & Security Solutions, Inc. 6.50%, 11/30/25 (a)		100		105
Mauser Packaging Solutions Holding Co. 5.50%, 4/15/24 (a)		500		503
Spirit AeroSystems, Inc. 7.50%, 4/15/25 (a)		200		203
Triumph Group, Inc. 6.25%, 9/15/24 (a)		250		213
TTM Technologies, Inc. 5.63%, 10/1/25 (a)		400		410
				2,085
Utilities (0.5%)
Calpine Corp. 5.25%, 6/1/26 (a)		250		260
				8,438
Variable Rate Senior Loan Interests (82.8%)
Basic Materials (2.7%)
Asplundh Tree Expert LLC, Term Loan B 3 Month USD LIBOR + 2.50%, 2.65%, 9/7/27 (b)		125		125
Chemours Company (The), Term Loan B2 3 Month USD LIBOR + 1.75%, 1.90%, 4/3/25 (b)		496		480
Cyanco Intermediate Corporation, 2020 Term Loan B 1 Month USD LIBOR + 3.50%, 3.65%, 3/16/25 (b)		496		491
Innophos, Inc., 2020 Term Loan B 1 Month USD LIBOR + 3.75%, 3.90%, 2/7/27 (b)		249		247
				1,343
Communications (14.4%)
ABG Intermediate Holdings 2 LLC, 2017 1st Lien Add-On Term Loan 3 Month USD LIBOR + 3.50%, 4.50%, 9/27/24 (b)		250		245
Avaya, Inc., 2018 Term Loan B 1 Month USD LIBOR + 4.25%, 4.40%, 12/15/24 (b)		500		498
Block Communications, Inc., 2020 Term Loan 3 Month USD LIBOR + 2.25%, 2.47%, 2/11/27 (b)		498		491

The accompanying notes are an integral part of the financial statements.
6

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Senior Loan Portfolio

	Face Amount (000)		Value (000)
Communications (cont'd)
CenturyLink, Inc., 2020 Term Loan B 1 Month USD LIBOR + 2.25%, 2.40%, 3/15/27 (b)	$	496	$	478
Clear Channel Outdoor Holdings, Inc., Term Loan B 3 Month USD LIBOR + 3.50%, 3.76%, 8/21/26 (b)		496		454
Cogeco Communications Finance (USA) II L.P., Term Loan B 1 Month USD LIBOR + 2.00%, 2.15%, 1/3/25 (b)		496		484
Coral-US Co-Borrower LLC, 2020 Term Loan B5 1 Month USD LIBOR + 2.25%, 2.40%, 1/31/28 (b)		500		485
Digicel International Finance Limited, Term Loan B 6 Month USD LIBOR + 3.25%, 3.80%, 5/28/24 (b)		248		219
Go Daddy Operating Co. LLC, 2020 Term Loan B3 1 Month USD LIBOR + 2.50%, 2.65%, 8/10/27 (b)		249		246
Hargray Communications Group, Inc., 2017 Term Loan B 1 Month USD LIBOR + 3.00%, 4.00%, 5/16/24 (b)		248		247
LCPR Loan Financing LLC, Term Loan B 1 Month USD LIBOR + 5.00%, 5.15%, 10/15/26 (b)		300		300
Level 3 Financing Inc., 2019 Term Loan B 1 Month USD LIBOR + 1.75%, 1.90%, 3/1/27 (b)		250		243
MH Sub I LLC, 2020 Incremental Term Loan 3 Month USD LIBOR + 3.75%, 4.75%, 9/13/24 (b)		100		99
NEP/NCP Holdco, Inc., 2018 1st Lien Term Loan 3 Month USD LIBOR + 3.25%, 3.40%, 10/20/25 (b)		496		430
PUG LLC, USD Term Loan 1 Month USD LIBOR + 3.50%, 3.65%, 2/12/27 (b)		695		617
Univision Communications Inc., Term Loan C5 1 Month USD LIBOR + 3.75%, 4.75%, 3/13/26 (b)		360		351
Virgin Media Bristol LLC, USD Term Loan N 1 Month USD LIBOR + 2.50%, 2.65%, 1/31/28 (b)		500		486
Zacapa SARL, 2018 1st Lien Term Loan B 3 Month USD LIBOR + 4.50%, 4.77%, 7/2/25 (b)		249		248

	Face Amount (000)		Value (000)
Ziggo Financing Partnership, USD Term Loan I 1 Month USD LIBOR + 2.50%, 2.65%, 4/30/28 (b)	$	500	$	482
				7,103
Consumer, Cyclical (15.7%)
1011778 B.C. Unlimited Liability Company, Term Loan B4 1 Month USD LIBOR + 1.75%, 1.90%, 11/19/26 (b)		248		239
Aimbridge Acquisition Co., Inc., 2019 Term Loan B 1 Month USD LIBOR + 3.75%, 3.89%, 2/2/26 (b)		223		201
Allegiant Travel Company, 2020 Term Loan 1 Month USD LIBOR + 3.00%, 3.25%, 2/5/24 (b)		497		464
American Airlines, Inc., 2017 Replacement Term Loan 1 Month USD LIBOR + 1.75%, 1.90%, 1/29/27 (b)		500		369
American Builders & Contractors Supply Co., Inc., 2019 Term Loan 1 Month USD LIBOR + 2.00%, 2.15%, 1/15/27 (b)		397		387
Aramark Services, Inc., 2019 Term Loan B4 1 Month USD LIBOR + 1.75%, 1.90%, 1/15/27 (b)		498		478
Burlington Coat Factory Warehouse Corporation, 2017 Term Loan B5 1 Month USD LIBOR + 1.75%, 1.91%, 11/17/24 (b)		250		244
BW Gas & Convenience Holdings LLC, Term Loan 1 Month USD LIBOR + 6.25%, 6.40%, 11/18/24 (b)		674		678
Carrols Restaurant Group, Inc., Term Loan B 3 Month USD LIBOR + 3.25%, 3.40% - 3.48%, 4/30/26 (b)		496		474
Core & Main LP, 2017 Term Loan B 3 Month USD LIBOR + 2.75%, 3.75%, 8/1/24 (b)		496		489
Delta 2 (LUX) S.a.r.l., Term Loan B 3 Month USD LIBOR + 2.50%, 3.50%, 2/1/24 (b)		500		487
Golden Nugget, Inc., 2017 Incremental Term Loan B 1 Month USD LIBOR + 2.50%, 2.65% - 3.25%, 10/4/23 (b)		545		490
Harbor Freight Tools USA, Inc., 2018 Term Loan B 3 Month USD LIBOR + 2.50%, 3.25%, 8/18/23 (b)		497		491

The accompanying notes are an integral part of the financial statements.
7

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Senior Loan Portfolio

	Face Amount (000)		Value (000)
Consumer, Cyclical (cont'd)
IRB Holding Corp, 2020 Term Loan B 1 Month USD LIBOR + 2.75%, 3.75%, 2/5/25 (b)	$	496	$	475
JetBlue Airways Corporation, Term Loan 3 Month USD LIBOR + 5.25%, 6.25%, 6/17/24 (b)		99		98
Lions Gate Capital Holdings LLC, 2018 Term Loan B 3 Month USD LIBOR + 2.25%, 2.40%, 3/24/25 (b)		244		236
Playa Resorts Holding BV, 2017 Term Loan B 1 Month USD LIBOR + 2.75%, 3.75%, 4/29/24 (b)		345		305
Scientific Games International, Inc., 2018 Term Loan B5 3 Month USD LIBOR + 2.75%, 2.90% - 3.61%, 8/14/24 (b)		496		468
Truck Hero, Inc., 1st Lien Term Loan 3 Month USD LIBOR + 3.75%, 3.90%, 4/22/24 (b)		496		482
WMG Acquisition Corp., 2018 Term Loan F 1 Month USD LIBOR + 2.12%, 2.27%, 11/1/23 (b)		155		152
				7,707
Consumer, Non-Cyclical (17.3%)
Acadia Healthcare Co., Inc., 2018 Term Loan B4 3 Month USD LIBOR + 2.50%, 2.65%, 2/16/23 (b)		496		493
Agiliti Health, Inc, Term Loan B 3 Month USD LIBOR + 3.00%, 3.15% - 3.19%, 1/4/26 (b)		496		483
Amneal Pharmaceuticals LLC, 2018 Term Loan B 1 Month USD LIBOR + 3.50%, 3.69%, 5/4/25 (b)		224		212
Bausch Health Cos., Inc., 2018 Term Loan B 3 Month USD LIBOR + 3.00%, 3.15%, 6/2/25 (b)		452		444
Creative Artists Agency LLC, 2019 Term Loan B 1 Month USD LIBOR + 3.75%, 3.90%, 11/27/26 (b)		496		478
DaVita, Inc., 2020 Term Loan B 1 Month USD LIBOR + 1.75%, 1.90%, 8/12/26 (b)		248		244
EyeCare Partners LLC, 2020 Delayed Draw Term Loan 3.75%, 2/18/27 (c)		76		72

	Face Amount (000)		Value (000)
EyeCare Partners LLC, 2020 Term Loan 1 Month USD LIBOR + 3.75%, 3.90%, 2/18/27 (b)	$	323	$	305
Froneri International Ltd., 2020 USD Term Loan 1 Month USD LIBOR + 2.25%, 2.40%, 1/31/27 (b)		499		480
Garda World Security Corp., 2019 1st Lien Term Loan B 3 Month USD LIBOR + 4.75%, 4.90%, 10/30/26 (b)		375		374
Gentiva Health Services, Inc., 2020 Term Loan 1 Month USD LIBOR + 3.25%, 3.44%, 7/2/25 (b)		498		488
Grifols Worldwide Operations USA, Inc., 2019 Term Loan B 1 Month USD LIBOR + 2.00%, 2.10%, 11/15/27 (b)		248		244
H Food Holdings LLC, 2018 Term Loan B 1 Month USD LIBOR + 3.68%, 3.83%, 5/23/25 (b)		244		238
HCA, Inc., Term Loan B12 1 Month USD LIBOR + 1.75%, 1.90%, 3/13/25 (b)		496		495
Jaguar Holding Company II, 2018 Term Loan 3 Month USD LIBOR + 2.50%, 3.50%, 8/18/22 (b)		245		245
Lineage Logistics Holdings LLC, 2018 Term Loan 3 Month USD LIBOR + 3.00%, 4.00%, 2/27/25 (b)		496		490
MMM Holdings, Inc., Term Loan B 1 Month USD LIBOR + 5.75, 6.75%, 12/24/26		100		100
Pearl Intermediate Parent LLC, 2018 1st Lien Term Loan 3 Month USD LIBOR + 2.75%, 2.90%, 2/14/25 (b)		496		481
Pearl Intermediate Parent LLC, 2018 Incremental Term Loan 3 Month USD LIBOR + 3.25%, 5.01%, 2/14/25 (b)		149		146
Refinitiv US Holdings, Inc., 2018 USD Term Loan 1 Month USD LIBOR + 3.25%, 3.40%, 10/1/25 (b)		298		296
Select Medical Corp., 2017 Term Loan B 1 Month USD LIBOR + 2.50%, 2.78%, 3/6/25 (b)		250		244
Surgery Center Holdings, Inc., 2017 Term Loan B 3 Month USD LIBOR + 3.25%, 4.25%, 9/3/24 (b)		744		704

The accompanying notes are an integral part of the financial statements.
8

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Senior Loan Portfolio

	Face Amount (000)		Value (000)
Consumer, Non-Cyclical (cont'd)
TMS International Corp., 2018 Term Loan B2 3 Month USD LIBOR + 2.75%, 3.75%, 8/14/24 (b)	$	496	$	486
US Foods, Inc., 2019 Term Loan B 3 Month USD LIBOR + 2.00%, 2.75%, 9/13/26 (b)		249		239
				8,481
Energy (3.4%)
Blackstone CQP Holdco LP, Term Loan B 3 Month USD LIBOR + 3.50%, 3.73%, 9/30/24 (b)		496		487
Lower Cadence Holdings LLC, Term Loan B 3 Month USD LIBOR + 4.00%, 4.15%, 5/22/26 (b)		496		461
Medallion Midland Acquisition LLC, 1st Lien Term Loan 3 Month USD LIBOR + 3.25%, 4.25%, 10/30/24 (b)		496		470
Stonepeak Lonestar Holdings LLC, Term Loan B 3 Month USD LIBOR + 4.50%, 4.77%, 10/19/26 (b)		244		241
				1,659
Finance (8.1%)
AqGen Ascensus, Inc., 2020 Term Loan 1 Month USD LIBOR + 4.00%, 5.00%, 12/13/26 (b)		150		149
Blackstone Mortgage Trust, Inc., 2019 New Term Loan 1 Month USD LIBOR + 2.25%, 2.41%, 4/23/26 (b)		496		476
Brookfield Property REIT, Inc., 1st Lien Term Loan B 3 Month USD LIBOR + 2.50%, 2.65%, 8/27/25 (b)		496		405
Charter Communications Operating LLC, 2019 Term Loan B1 1 Month USD LIBOR + 1.75%, 1.90%, 4/30/25 (b)		224		220
Citadel Securities LP, 2020 Term Loan B 1 Month USD LIBOR + 2.75%, 2.90%, 2/27/26 (b)		248		247
Hub International Limited, 2018 Term Loan B 3 Month USD LIBOR + 3.00%, 3.22% - 3.26%, 4/25/25 (b)		496		481
Illuminate Buyer LLC, Term Loan 1 Month USD LIBOR + 4.00%, 4.22%, 6/16/27 (b)		100		99
Jefferies Finance LLC, 2020 Incremental Term Loan B 9/30/27 (d)		250		248

	Face Amount (000)		Value (000)
Jefferies Finance LLC, 2019 Term Loan 1 Month USD LIBOR + 3.25%, 3.44%, 6/3/26 (b)	$	496	$	478
Sedgwick Claims Management Services, Inc., 2018 Term Loan B 3 Month USD LIBOR + 3.25%, 3.40%, 12/31/25 (b)		496		480
Vertical US Newco, Inc., Term Loan B 3 Month USD LIBOR + 4.25%, 4.57%, 7/30/27 (b)		400		397
VICI Properties 1 LLC, Replacement Term Loan B 1 Month USD LIBOR + 1.75%, 1.91%, 12/20/24 (b)		300		291
				3,971
Industrials (11.4%)
ACProducts, Inc., 2020 Term Loan B 1 Month USD LIBOR + 6.50%, 7.50%, 8/18/25 (b)		123		124
Brand Energy & Infrastructure Services, Inc., 2017 Term Loan 3 Month USD LIBOR + 4.25%, 5.25%, 6/21/24 (b)		397		371
Cornerstone Building Brands, Inc., 2018 Term Loan 1 Month USD LIBOR + 3.75%, 3.90%, 4/12/25 (b)		496		489
CPG International, Inc., 2017 Term Loan 3 Month USD LIBOR + 3.75%, 4.75%, 5/5/24 (b)		295		295
Flex Acquisition Company, Inc., 1st Lien Term Loan 3 Month USD LIBOR + 3.00%, 4.00%, 12/29/23 (b)		482		472
Generac Power Systems, Inc., 2019 Term Loan B 1 Month USD LIBOR + 1.75%, 1.91%, 12/13/26 (b)		500		498
Ingersoll-Rand Services Co., 2020 USD Spinco Term Loan 1 Month USD LIBOR + 1.75%, 1.90%, 3/1/27 (b)		249		241
Patriot Container Corp., 2018 1st Lien Term Loan 3/20/25 (d)		249		245
Quikrete Holdings, Inc., 2016 1st Lien Term Loan 1 Month USD LIBOR + 2.50%, 2.65%, 2/1/27 (b)		496		484
Reynolds Group Holdings, Inc., Term Loan 1 Month USD LIBOR + 2.75, 2.90%, 2/5/23 (b)		194		192
Tank Holding Corp., 2020 Term Loan 3/26/26 (d)		250		247
Titan Acquisition Limited, 2018 Term Loan B 3 Month USD LIBOR + 3.00%, 3.22%, 3/28/25 (b)		248		235

The accompanying notes are an integral part of the financial statements.
9

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Senior Loan Portfolio

	Face Amount (000)		Value (000)
Industrials (cont'd)
TransDigm, Inc., 2020 Term Loan F 1 Month USD LIBOR + 2.25%, 2.40%, 12/9/25 (b)	$	496	$	470
Trident TPI Holdings, Inc., 2017 USD Term Loan B1 3 Month USD LIBOR + 3.00%, 4.00%, 10/17/24 (b)		496		485
Tutor Perini Corporation, Term Loan B 3 Month USD LIBOR + 4.75%, 5.75%, 8/13/27 (b)		250		247
XPO Logistics, Inc., 2018 Refinancing Term Loan 1 Month USD LIBOR + 2.00%, 2.15%, 2/24/25 (b)		250		246
Zekelman Industries, Inc., 2020 Term Loan 1 Month USD LIBOR + 2.25%, 2.14%, 1/24/27 (b)		249		242
				5,583
Technology (9.6%)
Banff Merger Sub, Inc., 2018 USD Term Loan B 1 Month USD LIBOR + 4.25%, 4.40%, 10/2/25 (b)		398		388
By Crown Parent LLC, Term Loan B1 1 Month USD LIBOR + 3.00%, 4.00%, 1/31/26 (b)		349		346
Camelot U.S. Acquisition 1 Co., 2020 Incremental Term Loan B 10/30/26 (d)		125		125
DCert Buyer, Inc., 2019 Term Loan B 3 Month USD LIBOR + 4.00%, 4.15%, 10/16/26 (b)		249		246
Dell International LLC, 2019 Term Loan B 1 Month USD LIBOR + 2.00%, 2.75%, 9/19/25 (b)		245		244
Hyland Software, Inc., 2018 1st Lien Term Loan 7/1/24 (d)		150		149
McAfee LLC, 2018 USD Term Loan B 1 Month USD LIBOR + 3.75%, 3.90%, 9/30/24 (b)		497		495
Rackspace Hosting, Inc., 2017 Incremental 1st Lien Term Loan 3 Month USD LIBOR + 3.00%, 3.18% - 4.00%, 11/3/23 (b)		447		439
Redstone Buyer LLC, Term Loan 3 Month USD LIBOR + 5.00%, 6.00%, 9/1/27 (b)		400		399
Surf Holdings LLC, USD Term Loan 3 Month USD LIBOR + 3.50%, 3.75%, 3/5/27 (b)		499		489

	Face Amount (000)		Value (000)
Verifone Systems, Inc., 2018 1st Lien Term Loan 3 Month USD LIBOR + 4.00%, 4.25%, 8/20/25 (b)	$	497	$	447
VS Buyer LLC, Term Loan B 1 Month USD LIBOR + 3.25%, 3.40%, 2/28/27 (b)		498		491
Western Digital Corporation, 2018 Term Loan B4 3 Month USD LIBOR + 1.75%, 1.91%, 4/29/23 (b)		456		454
				4,712
Utilities (0.2%)
Pacific Gas & Electric Company, 2020 Term Loan 3 Month USD LIBOR + 4.50%, 5.50%, 6/23/25 (b)		100		98
				40,657
Total Fixed Income Securities (Cost $50,336)				49,095
	Shares
Short-Term Investment (0.1%)
Investment Company (0.1%)
Morgan Stanley Institutional Liquidity Funds — Government Portfolio — Institutional Class (See Note G) (Cost $55)		54,745		55
Total Investments (100.1%) (Cost $50,391) (e)				49,150
Liabilities in Excess of Other Assets (–0.1%)				(56	)
Net Assets (100.0%)			$	49,094

(a)  144A security — Certain conditions for public sale may exist. Unless otherwise noted, these securities are deemed to be liquid.

(b)  Floating or variable rate securities: The rates disclosed are as of September 30, 2020. For securities based on a published reference rate and spread, the reference rate and spread are indicated in the description in the Portfolio of Investments. Certain variable rate securities may not be based on a published reference rate and spread but are determined by the issuer or agent and are based on current market conditions. These securities do not indicate a reference rate and spread in their description in the Portfolio of Investments.

(c)  In addition to the term loan, the fund has an unfunded loan commitment of approximately $72,000, which could be extended at the option of the borrower. As of September 30, 2020, EyeCare Partners, LLC, did not draw down any of the commitment.

(d)  Unsettled Position. The contract rate does not take effect until settlement date.

(e)  At September 30, 2020, the aggregate cost for federal income tax purposes is approximately $50,406,000. The aggregate gross unrealized appreciation is approximately $299,000 and the aggregate gross unrealized depreciation is approximately $1,555,000, resulting in net unrealized depreciation of approximately $1,256,000.

LIBOR  London Interbank Offered Rate.

REIT  Real Estate Investment Trust.

USD  United States Dollar.

The accompanying notes are an integral part of the financial statements.
10

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Senior Loan Portfolio

Portfolio Composition

Classification	Percentage of Total Investments
Variable Rate Senior Loan Interests		82.7	%
Other*		17.2
Short-Term Investment		0.1
Total Investments		100.0	%

*  Industries and/or investment types representing less than 5% of total investments.

The accompanying notes are an integral part of the financial statements.
11

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Senior Loan Portfolio

Statement of Assets and Liabilities	September 30, 2020 (000)
Assets:
Investments in Securities of Unaffiliated Issuers, at Value (Cost $50,336)	$	49,095
Investment in Security of Affiliated Issuer, at Value (Cost $55)		55
Total Investments in Securities, at Value (Cost $50,391)		49,150
Receivable for Investments Sold		1,039
Interest Receivable		269
Prepaid Offering Costs		56
Due from Adviser		7
Receivable from Affiliate		—	@
Other Assets		7
Total Assets		50,528
Liabilities:
Payable for Investments Purchased		1,107
Payable for Offering Costs		151
Payable for Professional Fees		88
Payable for Unfunded Loan Commitments		76
Payable for Administration Fees		3
Payable for Custodian Fees		1
Payable for Transfer Agency Fees — Class I		—	@
Payable for Transfer Agency Fees — Class A		—	@
Payable for Transfer Agency Fees — Class C		—	@
Payable for Transfer Agency Fees — Class IS		—	@
Payable for Shareholder Services Fees — Class A		—	@
Payable for Distribution and Shareholder Services Fees — Class C		—	@
Other Liabilities		8
Total Liabilities		1,434
Net Assets	$	49,094
Net Assets Consist of:
Paid-in-Capital	$	50,946
Total Accumulated Loss		(1,852	)
Net Assets	$	49,094
CLASS I:
Net Assets	$	49,064
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		5,098,814
Net Asset Value, Offering and Redemption Price Per Share	$	9.62
CLASS A:
Net Assets	$	10
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		1,018
Net Asset Value, Redemption Price Per Share	$	9.62
Maximum Sales Load		3.25	%
Maximum Sales Charge	$	0.32
Maximum Offering Price Per Share	$	9.94
CLASS C:
Net Assets	$	10
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		1,014
Net Asset Value, Offering and Redemption Price Per Share	$	9.61
CLASS IS:
Net Assets	$	10
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		1,020
Net Asset Value, Offering and Redemption Price Per Share	$	9.62

@  Amount is less than $500.

The accompanying notes are an integral part of the financial statements.
12

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Senior Loan Portfolio

Statement of Operations	Period from January 31, 2020^ to September 30, 2020 (000)
Investment Income:
Interest from Securities of Unaffiliated Issuers	$	1,275
Dividends from Security of Affiliated Issuer (Note G)		51
Total Investment Income		1,326
Expenses:
Advisory Fees (Note B)		189
Professional Fees		125
Offering Costs		111
Administration Fees (Note C)		25
Shareholder Reporting Fees		13
Transfer Agency Fees — Class I (Note E)		1
Transfer Agency Fees — Class A (Note E)		1
Transfer Agency Fees — Class C (Note E)		1
Transfer Agency Fees — Class IS (Note E)		1
Pricing Fees		5
Custodian Fees (Note F)		2
Registration Fees		2
Trustees' Fees and Expenses		1
Shareholder Services Fees — Class A (Note D)		—	@
Distribution and Shareholder Services Fees — Class C (Note D)		—	@
Other Expenses		3
Total Expenses		480
Waiver of Advisory Fees (Note B)		(189	)
Expenses Reimbursed by Adviser (Note B)		(51	)
Rebate from Morgan Stanley Affiliate (Note G)		(8	)
Reimbursement of Class Specific Expenses — Class A (Note B)		(1	)
Reimbursement of Class Specific Expenses — Class C (Note B)		(1	)
Reimbursement of Class Specific Expenses — Class IS (Note B)		(1	)
Net Expenses		229
Net Investment Income		1,097
Realized Loss:
Investments Sold		(763	)
Change in Unrealized Appreciation (Depreciation):
Investments		(1,241	)
Net Realized Loss and Change in Unrealized Appreciation (Depreciation)		(2,004	)
Net Decrease in Net Assets Resulting from Operations	$	(907	)

^  Commencement of Operations.

@  Amount is less than $500.

The accompanying notes are an integral part of the financial statements.
13

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Senior Loan Portfolio

Statement of Changes in Net Assets	Period from January 31, 2020^ to September 30, 2020 (000)
Increase (Decrease) in Net Assets:
Operations:
Net Investment Income	$	1,097
Net Realized Loss		(763	)
Net Change in Unrealized Appreciation (Depreciation)		(1,241	)
Net Decrease in Net Assets Resulting from Operations		(907	)
Dividends and Distributions to Shareholders:
Class I		(945	)
Class A		(—	@)
Class C		(—	@)
Class IS		(—	@)
Total Dividends and Distributions to Shareholders		(945	)
Capital Share Transactions:(1)
Class I:
Subscribed		49,971
Distributions Reinvested		945
Class A:
Subscribed		10
Distributions Reinvested		—	@
Class C:
Subscribed		10
Distributions Reinvested		—	@
Class IS:
Subscribed		10
Distributions Reinvested		—	@
Net Increase in Net Assets Resulting from Capital Share Transactions		50,946
Total Increase in Net Assets		49,094
Net Assets:
Beginning of Period		—
End of Period	$	49,094
(1)   Capital Share Transactions:
Class I:
Shares Subscribed		4,997
Shares Issued on Distributions Reinvested		102
Net Increase in Class I Shares Outstanding		5,099
Class A:
Shares Subscribed		1
Shares Issued on Distributions Reinvested		—	@@
Net Increase in Class A Shares Outstanding		1
Class C:
Shares Subscribed		1
Shares Issued on Distributions Reinvested		—	@@
Net Increase in Class C Shares Outstanding		1
Class IS:
Shares Subscribed		1
Shares Issued on Distributions Reinvested		—	@@
Net Increase in Class IS Shares Outstanding		1

^  Commencement of Operations.

@  Amount is less than $500.

@@  Amount is less than 500 shares.

The accompanying notes are an integral part of the financial statements.
14

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Senior Loan Portfolio

	Class I
Selected Per Share Data and Ratios	Period from January 31, 2020(1) to September 30, 2020
Net Asset Value, Beginning of Period	$	10.00
Income (Loss) from Investment Operations:
Net Investment Income(2)		0.22
Net Realized and Unrealized Loss		(0.41	)
Total from Investment Operations		(0.19	)
Distributions from and/or in Excess of:
Net Investment Income		(0.19	)
Net Asset Value, End of Period	$	9.62
Total Return(3)		(1.84	)%(5)
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	49,064
Ratio of Expenses Before Expense Limitation		1.52	%(6)
Ratio of Expenses After Expense Limitation		0.73	%(4)(6)
Ratio of Net Investment Income		3.49	%(4)(6)
Ratio of Rebate from Morgan Stanley Affiliates		0.02	%(6)
Portfolio Turnover Rate		27	%(5)

(1)  Commencement of Operations.

(2)  Per share amount is based on average shares outstanding.

(3)  Calculated based on the net asset value as of the last business day of the period.

(4)  The Ratio of Expenses After Expense Limitation and Ratio of Net Investment Income reflect the rebate of certain Fund expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates."

(5)  Not annualized.

(6)  Annualized.

The accompanying notes are an integral part of the financial statements.
15

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Senior Loan Portfolio

	Class A
Selected Per Share Data and Ratios	Period from January 31, 2020(1) to September 30, 2020
Net Asset Value, Beginning of Period	$	10.00
Income (Loss) from Investment Operations:
Net Investment Income(2)		0.19
Net Realized and Unrealized Loss		(0.40	)
Total from Investment Operations		(0.21	)
Distributions from and/or in Excess of:
Net Investment Income		(0.17	)
Net Asset Value, End of Period	$	9.62
Total Return(3)		(2.07	)%(5)
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	10
Ratio of Expenses Before Expense Limitation		22.54	%(6)
Ratio of Expenses After Expense Limitation		1.13	%(4)(6)
Ratio of Net Investment Income		3.09	%(4)(6)
Ratio of Rebate from Morgan Stanley Affiliates		0.02	%(6)
Portfolio Turnover Rate		27	%(5)

(1)  Commencement of Operations.

(2)  Per share amount is based on average shares outstanding.

(3)  Calculated based on the net asset value which does not reflect sales charges, if applicable, as of the last business day of the period.

(4)  The Ratio of Expenses After Expense Limitation and Ratio of Net Investment Income reflect the rebate of certain Fund expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates."

(5)  Not annualized.

(6)  Annualized.

The accompanying notes are an integral part of the financial statements.
16

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Senior Loan Portfolio

	Class C
Selected Per Share Data and Ratios	Period from January 31, 2020(1) to September 30, 2020
Net Asset Value, Beginning of Period	$	10.00
Income (Loss) from Investment Operations:
Net Investment Income(2)		0.15
Net Realized and Unrealized Loss		(0.42	)
Total from Investment Operations		(0.27	)
Distributions from and/or in Excess of:
Net Investment Income		(0.12	)
Net Asset Value, End of Period	$	9.61
Total Return(3)		(2.59	)%(5)
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	10
Ratio of Expenses Before Expense Limitation		23.27	%(6)
Ratio of Expenses After Expense Limitation		1.88	%(4)(6)
Ratio of Net Investment Income		2.34	%(4)(6)
Ratio of Rebate from Morgan Stanley Affiliates		0.02	%(6)
Portfolio Turnover Rate		27	%(5)

(1)  Commencement of Operations.

(2)  Per share amount is based on average shares outstanding.

(3)  Calculated based on the net asset value which does not reflect sales charges, if applicable, as of the last business day of the period.

(4)  The Ratio of Expenses After Expense Limitation and Ratio of Net Investment Income reflect the rebate of certain Fund expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates."

(5)  Not annualized.

(6)  Annualized.

The accompanying notes are an integral part of the financial statements.
17

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Senior Loan Portfolio

	Class IS
Selected Per Share Data and Ratios	Period from January 31, 2020(1) to September 30, 2020
Net Asset Value, Beginning of Period	$	10.00
Income (Loss) from Investment Operations:
Net Investment Income(2)		0.22
Net Realized and Unrealized Loss		(0.41	)
Total from Investment Operations		(0.19	)
Distributions from and/or in Excess of:
Net Investment Income		(0.19	)
Net Asset Value, End of Period	$	9.62
Total Return(3)		(1.84	)%(5)
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	10
Ratio of Expenses Before Expense Limitation		22.19	%(6)
Ratio of Expenses After Expense Limitation		0.72	%(4)(6)
Ratio of Net Investment Income		3.49	%(4)(6)
Ratio of Rebate from Morgan Stanley Affiliates		0.02	%(6)
Portfolio Turnover Rate		27	%(5)

(1)  Commencement of Operations.

(2)  Per share amount is based on average shares outstanding.

(3)  Calculated based on the net asset value as of the last business day of the period.

(4)  The Ratio of Expenses After Expense Limitation and Ratio of Net Investment Income reflect the rebate of certain Fund expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates."

(5)  Not annualized.

(6)  Annualized.

The accompanying notes are an integral part of the financial statements.
18

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements

Morgan Stanley Institutional Fund Trust ("Trust'') is registered under the Investment Company Act of 1940, as amended (the "Act''), as an open-end management investment company. The Trust is comprised of twelve separate, active funds (individually referred to as a "Fund," collectively as the "Funds"). The Trust applies investment company accounting and reporting guidance. All Funds are considered diversified for purposes of the Act.

The accompanying financial statements relate to the Senior Loan Portfolio. The Fund seeks a high level of current income.

The Fund commenced operations on January 31, 2020 and offers four classes of shares — Class I, Class A, Class C and Class IS.

A. Significant Accounting Policies: The following significant accounting policies are in conformity with U.S. generally accepted accounting principles ("GAAP"). Such policies are consistently followed by the Trust in the preparation of its financial statements. GAAP may require management to make estimates and assumptions that affect the reported amounts and disclosures in the financial statements. Actual results may differ from those estimates.

In March 2017, the Financial Accounting Standards Board ("FASB") issued an Accounting Standard Update, ASU 2017-08, Receivables-Nonrefundable Fees and Other Costs (Subtopic 310-20), Premium Amortization on Purchased Callable Debt Securities (the "ASU") which amends the amortization period for certain purchased callable debt securities held at a premium, shortening such period to the earliest call date. The ASU does not require any accounting change for debt securities held at a discount; the discount continues to be amortized to maturity. The ASU is effective for fiscal years, and interim periods within those fiscal years, beginning after December 15, 2018. The Fund has adopted the ASU as of September 30, 2020 and it did not have an impact on the Fund's financial statements.

In March 2020, FASB issued an Accounting Standard Update, ASU 2020-04, Reference Rate Reform (Topic 848) — Facilitation of the Effects of Reference Rate Reform on Financial Reporting ("ASU 2020-04"), which provides optional, temporary relief with respect to the financial reporting of contracts subject to certain types of modifications due to the planned discontinuation of the London Interbank Offered Rate ("LIBOR") and other IBOR-based reference rates at the end of 2021. The temporary relief provided by ASU 2020-04 is effective for certain reference rate-related contract modifications

that occur during the period from March 12, 2020 through December 31, 2022. Management is evaluating the impact of ASU 2020-04 on the Fund's investments, derivatives, debt and other contracts that will undergo reference rate-related modifications as a result of the reference rate reform.

1.  Security Valuation: (1) Certain portfolio securities may be valued by an outside pricing service/vendor approved by the Trust's Board of Trustees (the "Trustees"). The pricing service/vendor may employ a pricing model that takes into account, among other things, bids, yield spreads and/or other market data and specific security characteristics. Alternatively, if a valuation is not available from an outside pricing service/vendor, and the security trades on an exchange, the security may be valued at its latest reported sale price (or at the exchange official closing price if such exchange reports an official closing price), prior to the time when assets are valued. If there are no sales on a given day and if there is no official exchange closing price for that day, the security is valued at the mean between the last reported bid and asked prices if such bid and asked prices are available in the relevant exchanges. If only bid prices are available then the latest bid price may be used. If Morgan Stanley Investment Management Inc. (the "Adviser"), a wholly-owned subsidiary of Morgan Stanley, determines that the price provided by the outside pricing service/vendor or exchange does not reflect the security's fair value or is unable to provide a price, prices from brokers or dealers may also be utilized. In these circumstances, the value of the security will be the mean of bid and asked prices obtained from brokers or dealers; (2) certain senior collateralized loans ("Senior Loans") are valued based on quotations received from an independent pricing service; (3) when market quotations are not readily available, including circumstances under which the Adviser determines that the closing price, last sale price or the mean between the last reported bid and asked prices are not reflective of a security's market value, portfolio securities are valued at their fair value as determined in good faith under procedures established by and under the general supervision of the Trustees. Occasionally, developments affecting the closing prices of securities and other assets may occur between the times at which valuations of such securities are determined (that is, close of the foreign market on which the securities trade) and the close of business of the New York Stock Exchange ("NYSE"). If developments occur during such periods that are expected to materially affect the value of such securities, such valuations may be

19

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

adjusted to reflect the estimated fair value of such securities as of the close of the NYSE, as determined in good faith by the Trustees or by the Adviser using a pricing service and/or procedures approved by the Trustees; and (4) investments in mutual funds, including the Morgan Stanley Institutional Liquidity Funds, are valued at the net asset value ("NAV") as of the close of each business day.

The Trustees have responsibility for determining in good faith the fair value of the investments, and the Trustees may appoint others, such as the Trust's Adviser or a valuation committee, to assist the Trustees in determining fair value and to make the actual calculations pursuant to the fair valuation methodologies previously approved by the Trustees. Under procedures approved by the Trustees, the Trust's Adviser has formed a Valuation Committee whose members are approved by the Trustees. The Valuation Committee provides administration and oversight of the Trust's valuation policies and procedures, which are reviewed at least annually by the Trustees. These procedures allow the Trust to utilize independent pricing services, quotations from securities and financial instrument dealers and other market sources to determine fair value.

2.  Fair Value Measurement: FASB Accounting Standards Codification^TM ("ASC") 820, "Fair Value Measurement" ("ASC 820"), defines fair value as the value that the Fund would receive to sell an investment or pay to transfer a liability in a timely transaction with an independent buyer in the principal market, or in the absence of a principal market, the most advantageous market for the investment or liability. ASC 820 establishes a three-tier hierarchy to distinguish between (1) inputs that reflect the assumptions market participants would use in valuing an asset or liability developed based on market data obtained from sources independent of the reporting entity (observable inputs) and (2) inputs that reflect the reporting entity's own assumptions about the assumptions market participants would use in valuing an asset or liability developed based on the best information available in the circumstances (unobservable inputs) and to establish classification of fair value measurements for disclosure purposes. Various inputs are used in determining the value of the Fund's investments. The inputs are summarized in the three broad levels listed below:

•  Level 1 – unadjusted quoted prices in active markets for identical investments

•  Level 2 – other significant observable inputs (including quoted prices for similar investments, interest rates, prepayment speeds, credit risk, etc.)

•  Level 3 – significant unobservable inputs including the Fund's own assumptions in determining the fair value of investments. Factors considered in making this determination may include, but are not limited to, information obtained by contacting the issuer, analysts, or the appropriate stock exchange (for exchange-traded securities), analysis of the issuer's financial statements or other available documents and, if necessary, available information concerning other securities in similar circumstances.

The inputs or methodology used for valuing securities are not necessarily an indication of the risk associated with investing in those securities and the determination of the significance of a particular input to the fair value measurement in its entirety requires judgment and considers factors specific to each security.

The following is a summary of the inputs used to value the Fund's investments as of September 30, 2020:

Investment Type	Level 1 Unadjusted quoted prices (000)		Level 2 Other significant observable inputs (000)		Level 3 Significant unobservable inputs (000)		Total (000)
Assets:
Fixed Income Securities
Corporate Bonds	$	—	$	8,438	$	—	$	8,438
Variable Rate Senior Loan Interests		—		40,657		—		40,657
Total Fixed Income Securities		—		49,095		—		49,095
Short-Term Investment
Investment Company		55		—		—		55
Total Assets	$	55	$	49,095	$	—	$	49,150

Transfers between investment levels may occur as the markets fluctuate and/or the availability of data used in an investment's valuation changes.

3.  Senior Loans: Senior Loans are loans made to borrowers that may be corporations, partnerships or other entities. These borrowers operate in a variety of industries and geographic regions, although most Senior Loans are made to borrowers that are organized or located in the U.S. Sen-

20

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

ior Loans generally are negotiated between a borrower and several financial institution lenders represented by one or more lenders acting as agent of all the lenders. The agent is responsible for negotiating the loan agreement that establishes the terms and conditions of the Senior Loan and the rights of the borrower and the lenders. The Fund may purchase assignments of portions of Senior Loans from third parties and may invest in participations in Senior Loans. Senior Loans also may take the form of debt obligations of borrowers issued directly to investors in the form of debt securities (i.e., Senior Notes).

The purchaser of an assignment typically succeeds to all the rights and obligations under the loan agreement of the assigning lender and becomes a lender under the loan agreement. Assignments may, however, be arranged through private negotiations, and the rights and obligations acquired by the purchaser of an assignment may differ from, and be more limited than, those held by the assigning lender.

When the Fund purchases a participation in a Senior Loan, the Fund will usually have a contractual relationship only with the lender selling the participation and not with the borrower. The Fund may have the right to receive payments of principal, interest and any fees to which it is entitled only from the lender selling the participation and only upon receipt by the lender of such payments from the borrower. As a result, the Fund may assume the credit risk of both the borrower and the lender selling the participation. In the event of insolvency of the lender selling a participation, the Fund may be treated as a general creditor of the lender.

The Fund's investment in loans may include unfunded loan commitments, which are contractual obligations for funding. Unfunded loan commitments represent a future obligation in full, even though a percentage of the committed amount may not be utilized by the borrower. Unfunded loan commitments are reflected as a liability on the Statement of Assets and Liabilities.

4.  Indemnifications: The Trust enters into contracts that contain a variety of indemnifications. The Trust's maximum exposure under these arrangements is unknown. However, the Trust has not had prior claims or losses pursuant to these contracts and expects the risk of loss to be remote.

5.  Dividends and Distributions to Shareholders: Dividends and distributions to shareholders are recorded on the ex-dividend date. Dividends from net investment income, if any, are declared and paid monthly. Net realized capital gains, if any, are distributed at least annually.

6.  Security Transactions, Income and Expenses: Security transactions are accounted for on the trade date (date the order to buy or sell is executed). Realized gains and losses on the sale of investment securities are determined on the specific identified cost method. When the Fund buys an interest in a Senior Loan, it may receive a commitment fee which is paid to lenders on an ongoing basis based upon the undrawn portion committed by the lenders of the underlying Senior Loan. The Fund accrues the commitment fee over the expected term of the loan. When the Fund sells an interest in a Senior Loan, it may be required to pay fees or commissions to the purchaser of the interest. Fees received in connection with loan amendments are accrued as earned. Dividend income and other distributions are recorded on the ex-dividend date (except for certain foreign dividends which may be recorded as soon as the Fund is informed of such dividends) net of applicable withholding taxes. Interest income is recognized on the accrual basis except where collection is in doubt. Discounts are accreted and premiums are amortized over the life of the respective securities. Most expenses of the Fund can be directly attributed to a particular Fund. Expenses which cannot be directly attributed are apportioned among the Funds based upon relative net assets or other appropriate methods. Income, expenses (other than class specific expenses — distribution and shareholder services, transfer agency and sub transfer agency fees) and realized and unrealized gains or losses are allocated to each class of shares based upon their relative net assets.

B. Advisory Fees: The Adviser, a wholly-owned subsidiary of Morgan Stanley, provides the Fund with advisory services under the terms of an Investment Advisory Agreement, paid quarterly, at the annual rate based on the daily net assets as follows:

First $1 billion			Next $1.5 billion			Over $2.5 billion
	0.60	%		0.55	%		0.50	%

21

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

For the period ended September 30, 2020, the advisory fee rate (net of waivers/rebate) was equivalent to an annual effective rate of 0.00% of the Fund's average daily net assets.

The Adviser has agreed to reduce its advisory fee and/or reimburse the Fund so that total annual Fund operating expenses, excluding certain investment related expenses, taxes, interest and other extraordinary expenses (including litigation), will not exceed 0.80% for Class I shares, 1.15% for Class A shares, 1.90% for Class C shares and 0.75% for Class IS shares. The fee waivers and/or expense reimbursements will continue for at least one year from the date of the Fund's prospectus or until such time as the Trustees act to discontinue all or a portion of such waivers and/or reimbursements when they deem such action is appropriate. For the period ended September 30, 2020, approximately $189,000 of advisory fees were waived and approximately $54,000 of other expenses were reimbursed by the Adviser pursuant to this arrangement.

C. Administration Fees: The Adviser also serves as Administrator to the Trust and provides administrative services pursuant to an Administration Agreement for an annual fee, accrued daily and paid monthly, of 0.08% of the Fund's average daily net assets. Under a Sub-Administration Agreement between the Administrator and State Street Bank and Trust Company ("State Street"), State Street provides certain administrative services to the Trust. For such services, the Administrator pays State Street a portion of the fee the Administrator receives from the Fund.

D. Distribution and Shareholder Services Fees: Morgan Stanley Distribution, Inc. ("MSDI" or the "Distributor"), a wholly-owned subsidiary of the Adviser, and an indirect subsidiary of Morgan Stanley, serves as the Trust's Distributor of Fund shares pursuant to a Distribution Agreement. The Trust has adopted a Shareholder Services Plan with respect to Class A shares pursuant to Rule 12b-1 under the Act. Under the Shareholder Services Plan, the Fund pays the Distributor a shareholder services fee, accrued daily and paid monthly, at an annual rate of 0.25% of the Fund's average daily net assets attributable to Class A shares.

The Trust has adopted a Distribution and Shareholder Services Plan with respect to Class C shares pursuant to Rule 12b-1 under the Act. Under the Distribution and Shareholder Services Plan, the Fund pays the Distributor a distribution fee, accrued daily and paid monthly, at an annual rate of 0.75% and a shareholder services fee, accrued daily and paid monthly, at an

annual rate of 0.25% of the Fund's average daily net assets attributable to Class C shares.

The distribution and shareholder services fees are used to support the expenses associated with servicing and maintaining accounts. The Distributor may compensate other parties for providing shareholder support services to investors who purchase Class A and Class C shares.

E. Dividend Disbursing and Transfer/Co-Transfer Agent: The Trust's dividend disbursing and transfer agent is DST Asset Manager Solutions, Inc. ("DST"). Pursuant to a Transfer Agency Agreement, the Trust pays DST a fee based on the number of classes, accounts and transactions relating to the Funds of the Trust.

Morgan Stanley Services Company Inc. serves as Co-Transfer Agent and provides certain transfer agency services to the Fund with respect to certain direct transactions with the Fund.

F. Custodian Fees: State Street (the "Custodian") also serves as Custodian for the Trust in accordance with a Custodian Agreement. The Custodian holds cash, securities and other assets of the Trust as required by the Act. Custody fees are payable monthly based on assets held in custody, investment purchases and sales activity and account maintenance fees, plus reimbursement for certain out-of-pocket expenses.

G. Security Transactions and Transactions with Affiliates: For the period ended September 30, 2020, purchases and sales of investment securities for the Fund, other than long-term U.S. Government securities and short-term investments were approximately $62,997,000 and $11,906,000, respectively. There were no purchases and sales of long-term U.S. Government securities for the period ended September 30, 2020.

The Fund invests in the Institutional Class of the Morgan Stanley Institutional Liquidity Funds — Government Portfolio (the "Liquidity Funds"), an open-end management investment company managed by the Adviser. Advisory fees paid by the Fund are reduced by an amount equal to its pro-rata share of the advisory and administration fees paid by the Fund due to its investment in the Liquidity Funds. For the period ended September 30, 2020, advisory fees paid were reduced by approximately $8,000 relating to the Fund's investment in the Liquidity Funds.

22

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

A summary of the Fund's transactions in shares of affiliated investments during the period ended September 30, 2020 is as follows:

Affiliated Investment Company	Value January 31, 2020 (000)		Purchases at Cost (000)		Proceeds from Sales (000)		Dividend Income (000)
Liquidity Funds	$	—	$	57,630	$	57,575	$	51

Affiliated Investment Company (cont'd)	Realized Gain (Loss) (000)		Change in Unrealized Appreciation (Depreciation) (000)		Value September 30, 2020 (000)
Liquidity Funds	$	—	$	—	$	55

The Fund is permitted to purchase and sell securities ("cross-trade") from and to other Morgan Stanley funds as well as other funds and client accounts for which the Adviser or an affiliate of the Adviser serves as investment adviser, pursuant to procedures approved by the Trustees in compliance with Rule 17a-7 under the Act (the "Rule"). Each cross-trade is executed at the current market price in compliance with provisions of the Rule. For the period ended September 30, 2020, the Fund did not engage in any cross-trade transactions.

The Fund has an unfunded Deferred Compensation Plan (the "Compensation Plan"), which allows each independent Trustee to defer payment of all, or a portion, of the fees he or she receives for serving on the Board of Trustees. Each eligible Trustee generally may elect to have the deferred amounts credited with a return equal to the total return on one or more of the Morgan Stanley funds that are offered as investment options under the Compensation Plan. Appreciation/depreciation and distributions received from these investments are recorded with an offsetting increase/decrease in the deferred compensation obligation and do not affect the NAV of the Fund.

H. Federal Income Taxes: It is the Fund's intention to continue to qualify as a regulated investment company and distribute all of its taxable and tax-exempt income. Accordingly, no provision for federal income taxes is required in the financial statements.

The Fund may be subject to taxes imposed by countries in which it invests. Such taxes are generally based on income and/or capital gains earned or repatriated. Taxes are accrued based on net investment income, net realized gains and net unrealized appreciation as such income and/or gains are earned. Taxes may also be based on transactions in foreign currency and are accrued based on the value of investments denominated in such currency.

FASB ASC 740-10, "Income Taxes — Overall", sets forth a minimum threshold for financial statement recognition of the benefit of a tax position taken or expected to be taken in a tax return. Management has concluded there are no significant uncertain tax positions that would require recognition in the financial statements. If applicable, the Fund recognizes interest accrued related to unrecognized tax benefits in "Interest Expense" and penalties in "Other Expenses" in the Statement of Operations. The Fund files tax returns with the U.S. Internal Revenue Service, New York and various states. The tax period ended September 30, 2020, remains subject to examination by taxing authorities.

The tax character of distributions paid may differ from the character of distributions shown for GAAP purposes due to short-term capital gains being treated as ordinary income for tax purposes. The tax character of distributions paid during fiscal year 2020 was as follows:

2020 Distributions Paid From:
Ordinary Income (000)
$	945

The amount and character of income and gains to be distributed are determined in accordance with income tax regulations which may differ from GAAP. These book/tax differences are either considered temporary or permanent in nature.

Temporary differences are attributable to differing book and tax treatments for the timing of the recognition of gains (losses) on certain investment transactions and the timing of the deductibility of certain expenses.

Permanent differences, due to a nondeductible expense, resulted in the following reclassifications among the components of net assets at September 30, 2020:

Total Accumulated Loss (000)			Paid-in- Capital (000)
$	—	@	$	(—	@)

@ Amount is less than $500.

At September 30, 2020, the components of distributable earnings for the Fund on a tax basis were as follows:

Undistributed Ordinary Income (000)		Undistributed Long-Term Capital Gain (000)
$	275	$	—

23

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

At September 30, 2020, the Fund had available for federal income tax purposes unused short-term capital losses of approximately $765,000 that do not have an expiration date.

To the extent that capital loss carryforwards are used to offset any future capital gains realized, no capital gains tax liability will be incurred by the Fund for gains realized and not distributed. To the extent that capital gains are offset, such gains will not be distributed to the shareholders.

I. Credit Facility: The Trust and other Morgan Stanley funds participated in a $300,000,000 committed, unsecured revolving line of credit facility (the "Facility") with State Street. This Facility is to be used for temporary emergency purposes or funding of shareholder redemption requests. The interest rate on borrowings is based on the federal funds rate or 1 month LIBOR rate plus a spread. The Facility also has a commitment fee of 0.25% per annum based on the unused portion of the Facility. During the period ended September 30, 2020, the Fund did not have any borrowings under the Facility.

J. Other: At September 30, 2020, the Fund did not have record owners of 10% or greater.

K. Market Risk: Certain impacts to public health conditions particular to the coronavirus (COVID-19) outbreak could impact the operations and financial performance of certain of the Fund's investments. The extent of the impact to the financial performance of the Fund's investments will depend on future developments, including (i) the duration and spread of the outbreak, (ii) the restrictions and advisories, (iii) the effects on the financial markets, and (iv) the effects on the economy overall, all of which are highly uncertain and cannot be predicted. If the financial performance of the Fund's investments is impacted because of these factors for an extended period, the Fund's investment results may be adversely affected.

L. LIBOR Risk: The Fund's investments, payment obligations and financing terms may be based on floating rates, such as London Interbank Offer Rate ("LIBOR"), Euro Interbank Offered Rate and other similar types of reference rates (each, a "Reference Rate"). These Reference Rates are generally intended to represent the rate at which contributing banks may obtain short-term borrowings from each other within certain financial markets. On July 27, 2017, the Chief Executive of the UK Financial Conduct Authority ("FCA"), which regulates LIBOR, announced that the FCA will no longer persuade nor require banks to submit rates for the calculation of LIBOR and certain other Reference Rates after 2021. Such announcement

indicates that the continuation of LIBOR and other Reference Rates on the current basis cannot and will not be guaranteed after the end of 2021. This announcement and any additional regulatory or market changes may have an adverse impact on the Fund or its investments.

In advance of 2022, regulators and market participants are currently engaged in identifying successor Reference Rates ("Alternative Reference Rates"). Additionally, prior to the end of 2021, it is expected that market participants will focus on the transition mechanisms by which the Reference Rates in existing contracts or instruments may be amended, whether through marketwide protocols, fallback contractual provisions, bespoke negotiations or amendments or otherwise. Nonetheless, the termination of certain Reference Rates presents risks to the Fund. At this time, it is not possible to completely identify or predict the effect of any such changes, any establishment of Alternative Reference Rates or any other reforms to Reference Rates that may be enacted in the UK or elsewhere. The elimination of a Reference Rate or any other changes or reforms to the determination or supervision of Reference Rates could have an adverse impact on the market for or value of any securities or payments linked to those Reference Rates and other financial obligations held by the Fund or on its overall financial condition or results of operations.

24

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Report of Independent Registered Public Accounting Firm

To the Shareholders and Board of Trustees of
Morgan Stanley Institutional Fund Trust —
Senior Loan Portfolio

Opinion on the Financial Statements

We have audited the accompanying statement of assets and liabilities of Senior Loan Portfolio (the "Fund") (one of the funds constituting Morgan Stanley Institutional Fund Trust (the "Trust")), including the portfolio of investments, as of September 30, 2020, and the related statements of operations and changes in net assets and the financial highlights for the period from January 31, 2020 (commencement of operations) through September 30, 2020 and the related notes (collectively referred to as the "financial statements"). In our opinion, the financial statements present fairly, in all material respects, the financial position of Senior Loan Portfolio (one of the funds constituting Morgan Stanley Institutional Fund Trust) at September 30, 2020, the results of its operations and the changes in its net assets and its financial highlights for the period from January 31, 2020 (commencement of operations) through September 30, 2020, in conformity with U.S. generally accepted accounting principles.

Basis for Opinion

These financial statements are the responsibility of the Trust's management. Our responsibility is to express an opinion on the Fund's financial statements based on our audit. We are a public accounting firm registered with the Public Company Accounting Oversight Board (United States) ("PCAOB") and are required to be independent with respect to the Trust in accordance with the U.S. federal securities law and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB.

We conducted our audit in accordance with the standards of the PCAOB. Those standards require that we plan and perform the audit to obtain reasonable assurance about whether the financial statements are free of material misstatement, whether due to error or fraud. The Trust is not required to have, nor were we engaged to perform, an audit of the Trust's internal control over financial reporting. As part of our audit, we are required to obtain an understanding of internal control over financial reporting, but not for the purpose of expressing an opinion on the effectiveness of the Trust's internal control over financial reporting. Accordingly, we express no such opinion.

Our audit included performing procedures to assess the risks of material misstatement of the financial statements, whether due to error or fraud, and performing procedures that respond to those risks. Such procedures included examining, on a test basis, evidence regarding the amounts and disclosures in the financial statements. Our procedures included confirmation of securities owned as of September 30, 2020 by correspondence with the custodian and brokers or by other appropriate auditing procedures where replies from brokers were not received. Our audit also included evaluating the accounting principles used and significant estimates made by management, as well as evaluating the overall presentation of the financial statements. We believe that our audit provides a reasonable basis for our opinion.

We have served as the auditor of one or more Morgan Stanley investment companies since 2000.
Boston, Massachusetts
November 24, 2020

25

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Advisory Agreement Approval (unaudited)

The Board considered the following factors at the time of approval of the contracts which occurred prior to commencement of operations.

Nature, Extent and Quality of Services

The Board reviewed and considered the nature and extent of the investment advisory services to be provided by the Adviser under the advisory agreement, including portfolio management, investment research and equity and fixed income securities trading. The Board also reviewed and considered the nature and extent of the non-advisory, administrative services to be provided by the Administrator under the administration agreement, including accounting, operations, clerical, bookkeeping, compliance, business management and planning, legal services and the provision of supplies, office space and utilities at the Adviser's expense. The Board also considered the Adviser's investment in personnel and infrastructure that benefits the Fund. (The Adviser and Administrator together are referred to as the "Adviser" and the advisory and administration agreements together are referred to as the "Management Agreement.") The Board also considered that the Adviser serves a variety of other investment advisory clients and has experience overseeing service providers.

The Board reviewed and considered the qualifications of the portfolio managers, the senior administrative managers and other key personnel of the Adviser who will provide the advisory and administrative services to the Fund. The Board determined that the Adviser's portfolio managers and key personnel are well qualified by education and/or training and experience to perform the services in an efficient and professional manner. The Board concluded that the nature and extent of the advisory and administrative services to be provided were necessary and appropriate for the conduct of the business and investment activities of the Fund and supported its decision to approve the Management Agreement.

Performance, Fees and Expenses of the Fund

The Board considered that the Adviser plans to arrange for a public offering of shares of the Fund to raise assets for investment and that the offering had not yet begun and concluded that, since the Fund currently had no assets to invest (other than seed capital required under the Investment Company Act) and had no track record of performance, this was not a factor it needed to address at the present time.

The Board reviewed the advisory and administrative fee rates (the "management fee rates") proposed to be paid by the Fund under the Management Agreement relative to comparable funds advised by the Adviser, when applicable, and compared to their peers as determined by the Adviser, and reviewed the anticipated total expense ratio of the Fund. The Board considered that the Fund requires the Adviser to develop processes, invest in additional resources and incur additional risks to successfully manage the Fund and concluded that the proposed management fee rate and anticipated total expense ratio would be competitive with its peer group averages.

Economies of Scale

The Board considered the growth prospects of the Fund and the structure of the proposed management fee schedule, which does include breakpoints. The Board considered that the Fund's potential growth was uncertain and concluded that it would be premature to consider economies of scale as a factor in approving the Management Agreement at the present time.

Profitability of the Adviser and Affiliates

Since the Fund had not begun operations and had not paid any fees to the Adviser, the Board concluded that this was not a factor that needed to be considered at the present time.

Other Benefits of the Relationship

The Board considered other direct and indirect benefits to the Adviser and/or its affiliates to be derived from their relationship with the Fund and other funds advised by the Adviser. These benefits may include, among other things, fees for trading, distribution and/or shareholder servicing and for transaction processing and reporting platforms used by securities lending agents, and research received by the Adviser generated from commission dollars spent on funds' portfolio trading. Since the Fund had not begun operations and had not paid any fees to the Adviser, the Board concluded that these benefits were not a factor that needed to be considered at the present time.

26

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Advisory Agreement Approval (unaudited) (cont'd)

Resources of the Adviser and Historical Relationship Between the Fund and the Adviser

The Board considered whether the Adviser is financially sound and has the resources necessary to perform its obligations under the Management Agreement. The Board also reviewed and considered the organizational structure of the Adviser, the policies and procedures formulated and adopted by the Adviser for managing the Fund's operations and the Board's confidence in the competence and integrity of the senior managers and key personnel of the Adviser. The Board concluded that the Adviser has the financial resources necessary to fulfill its obligations under the Management Agreement and that it is beneficial for the Fund to enter into this relationship with the Adviser.

Other Factors and Current Trends

The Board considered the controls and procedures adopted and implemented by the Adviser and monitored by the Fund's Chief Compliance Officer and concluded that the conduct of business by the Adviser indicates a good faith effort on its part to adhere to high ethical standards in the conduct of the Fund's business.

As part of the Board's review, the Board received information from management on the impact of COVID-19 on the firm generally and the Adviser and the Fund in particular including, among other information, the pandemic's current and expected impact on the Fund's performance and operations.

General Conclusion

After considering and weighing all of the above factors, with various written materials and verbal information presented by the Adviser, the Board concluded that it would be in the best interest of the Fund and its future shareholders to approve the Management Agreement, which will remain in effect for two years and thereafter must be approved annually by the Board of the Fund if it is to continue in effect. In reaching this conclusion the Board did not give particular weight to any single piece of information or factor referenced above. It is possible that individual Board members may have weighed these factors, and the information presented, differently in reaching their individual decisions to approve the Management Agreement.

27

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Liquidity Risk Management Program (unaudited)

In compliance with Rule 22e-4 under the Investment Company Act of 1940, as amended (the "Liquidity Rule"), the Fund has adopted and implemented a liquidity risk management program (the "Program"), which is reasonably designed to assess and manage the risk that the Fund could not meet requests to redeem shares issued by the Fund without significant dilution of remaining investors' interests in the Fund (i.e., liquidity risk). The Fund's Board of Trustees (the "Board") previously approved the designation of the Liquidity Risk Subcommittee (the "LRS") as Program administrator. The LRS is comprised of representatives from various divisions within Morgan Stanley Investment Management.

At a meeting held on April 22-23, 2020, the Board reviewed a written report prepared by the LRS that addressed the Program's operation and assessed its adequacy, and effectiveness of implementation for the period from December 1, 2018, through December 31, 2019, as required under the Liquidity Rule. The report concluded that the Program operated effectively and was adequately and effectively implemented in all material aspects, and that the relevant controls and safeguards were appropriately designed to enable the LRS to administer the Program in compliance with the Liquidity Rule.

In accordance with the Program, the LRS assessed each Fund's liquidity risk no less frequently than annually taking into consideration certain factors, as applicable, such as (i) investment strategy and liquidity of portfolio investments, (ii) short-term and long-term cash flow projections and (iii) holdings of cash and cash equivalents and borrowing arrangements and other funding sources. Certain factors are considered under both normal and reasonably foreseeable stressed conditions.

Each Fund portfolio investment is classified into one of four liquidity categories, which classification is assessed at least monthly by the LRS. The classification is based on a determination of the number of days it is reasonably expected to take to convert the investment into cash, or sell or dispose of the investment, in current market conditions without significantly changing the market value of the investment. Liquidity classification determinations take into account various market, trading and investment-specific considerations, as well as market depth, and in some cases utilize third-party vendor data.

The Liquidity Rule limits a fund's investments in illiquid investments to 15% of its net assets and requires funds that do not primarily hold assets that are highly liquid investments to determine and maintain a minimum percentage of the fund's net assets to be invested in highly liquid investments (highly liquid investment minimum or "HLIM"). The LRS believes that the Program includes provisions reasonably designed to review, monitor and comply with the 15% limit on illiquid investments and for determining, periodically reviewing and complying with the HLIM requirement, as applicable.

There can be no assurance that the Program will achieve its objectives under all circumstances in the future. Please refer to the Fund's prospectus for more information regarding the Fund's exposure to liquidity risk and other risks to which it may be subject.

28

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Privacy Notice (unaudited)  April 2019

FACTS	WHAT DOES MSIM DO WITH YOUR PERSONAL INFORMATION?
Why?	Financial companies choose how they share your personal information. Federal law gives consumers the right to limit some but not all sharing. Federal law also requires us to tell you how we collect, share, and protect your personal information. Please read this notice carefully to understand what we do.
What?	The types of personal information we collect and share depend on the product or service you have with us. This information can include: n Social Security number and income n investment experience and risk tolerance n checking account number and wire transfer instructions
How?	All financial companies need to share customers' personal information to run their everyday business. In the section below, we list the reasons financial companies can share their customers' personal information; the reasons MSIM chooses to share; and whether you can limit this sharing.

Reasons we can share your personal information	Does MSIM share?	Can you limit this sharing?
For our everyday business purposes — such as to process your transactions, maintain your account(s), respond to court orders and legal investigations, or report to credit bureaus	Yes	No
For our marketing purposes — to offer our products and services to you	Yes	No
For joint marketing with other financial companies	No	We don't share
For our affiliates' everyday business purposes — information about your transactions and experiences	Yes	No
For our affiliates' everyday business purposes — information about your creditworthiness	No	We don't share
For our affiliates to market to you	No	We don't share
For non-affiliates to market to you	No	We don't share

Questions? Call toll-free (844) 312-6327 or email: imprivacyinquiries@morganstanley.com

Who we are

Who is providing this notice? Morgan Stanley Investment Management, Inc. and its affiliated registered investment advisers, registered broker-dealers, and registered and unregistered funds ("MSIM")

29

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Privacy Notice (unaudited) (cont'd)  April 2019

What we do

How does MSIM protect my personal information?	To protect your personal information from unauthorized access and use, we use security measures that comply with federal law. These measures include computer safeguards and secured files and buildings. We have policies governing the proper handling of customer information by personnel and requiring third parties that provide support to adhere to appropriate security standards with respect to such information.
How does MSIM collect my personal information?	We collect your personal information, for example, when you n open an account or make deposits or withdrawals from your account n buy securities from us or make a wire transfer n give us your contact information We also collect your personal information from others, such as credit bureaus, affiliates, or other companies.
Why can't I limit all sharing?	Federal law gives you the right to limit only n sharing for affiliates' everyday business purposes — information about your creditworthiness n affiliates from using your information to market to you n sharing for non-affiliates to market to you State laws and individual companies may give you additional rights to limit sharing. See below for more on your rights under state law.

Definitions

Affiliates	Companies related by common ownership or control. They can be financial and non-financial companies. n Our affiliates include companies with a Morgan Stanley name and financial companies such as Morgan Stanley Smith Barney LLC and Morgan Stanley & Co.
Non-affiliates	Companies not related by common ownership or control. They can be financial and non-financial companies. n MSIM does not share with non-affiliates so they can market to you.
Joint marketing	A formal agreement between non-affiliated financial companies that together market financial products or services to you. n MSIM doesn't jointly market

Other Important Information

Vermont: Except as permitted by law, we will not share personal information we collect about Vermont residents with Non-affiliates unless you provide us with your written consent to share such information.

California: Except as permitted by law, we will not share personal information we collect about California residents with Non-affiliates and we will limit sharing such personal information with our Affiliates to comply with California privacy laws that apply to us.

30

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited)

Independent Trustees:

Name, Address and Birth Year of Independent Trustee	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years and Other Relevant Professional Experience	Number of Funds in Fund Complex Overseen by Independent Trustee**	Other Directorships Held by Independent Trustee***
Frank L. Bowman c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1944	Trustee	Since August 2006	President, Strategic Decisions, LLC (consulting) (since February 2009); Director or Trustee of various Morgan Stanley Funds (since August 2006); Chairperson of the Compliance and Insurance Committee (since October 2015); formerly, Chairperson of the Insurance Sub-Committee of the Compliance and Insurance Committee (2007-2015); served as President and Chief Executive Officer of the Nuclear Energy Institute (policy organization) (February 2005-November 2008); retired as Admiral, U.S. Navy after serving over 38 years on active duty including 8 years as Director of the Naval Nuclear Propulsion Program in the Department of the Navy and the U.S. Department of Energy (1996-2004); served as Chief of Naval Personnel (July 1994-September 1996) and on the Joint Staff as Director of Political Military Affairs (June 1992-July 1994); knighted as Honorary Knight Commander of the Most Excellent Order of the British Empire; awarded the Officier de l'Orde National du Mérite by the French Government; elected to the National Academy of Engineering (2009).	86	Director of Naval and Nuclear Technologies LLP; Director Emeritus of the Armed Services YMCA; Member of the National Security Advisory Council of the Center for U.S. Global Engagement and a member of the CNA Military Advisory Board; Trustee of Fairhaven United Methodist Church; Member of the Board of Advisors of the Dolphin Scholarship Foundation; Director of other various non-profit organizations; Formerly, Director of BP p.l.c. (November 2010-May 2019).
Kathleen A. Dennis c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1953	Trustee	Since August 2006	President, Cedarwood Associates (mutual fund and investment management consulting) (since July 2006); Chairperson of the Liquidity and Alternatives Sub-Committee of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 2006); formerly, Senior Managing Director of Victory Capital Management (1993-2006).	86	Director of various non-profit organizations.
Nancy C. Everett c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1955	Trustee	Since January 2015	Chief Executive Officer, Virginia Commonwealth University Investment Company (since November 2015); Owner, OBIR, LLC (institutional investment management consulting) (since June 2014); formerly, Managing Director, BlackRock, Inc. (February 2011-December 2013); and Chief Executive Officer, General Motors Asset Management (a/k/a Promark Global Advisors, Inc.) (June 2005-May 2010).	87	Formerly, Member of Virginia Commonwealth University School of Business Foundation (2005-2016); Member of Virginia Commonwealth University Board of Visitors (2013-2015); Member of Committee on Directors for Emerging Markets Growth Fund, Inc. (2007-2010); Chairperson of Performance Equity Management, LLC (2006-2010); and Chairperson, GMAM Absolute Return Strategies Fund, LLC (2006-2010).

31

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Address and Birth Year of Independent Trustee	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years and Other Relevant Professional Experience	Number of Funds in Fund Complex Overseen by Independent Trustee**	Other Directorships Held by Independent Trustee***
Jakki L. Haussler c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1957	Trustee	Since January 2015	Chairman, Opus Capital Group (since January 1996); formerly, Chief Executive Officer, Opus Capital Group (1996-2019); Director, Capvest Venture Fund, LP (May 2000-December 2011); Partner, Adena Ventures, LP (July 1999-December 2010); Director, The Victory Funds (February 2005-July 2008).	87	Director of Service Corporation International and Member, Audit Committee and Investment Committee; Director of Cincinnati Bell Inc. and Member, Audit Committee and Governance and Nominating Committee; Director of Northern Kentucky University Foundation and Member, Investment Committee; Member of Chase College of Law Transactional Law Practice Center Board of Advisors; Director of Chase College of Law Board of Visitors; formerly, Member, University of Cincinnati Foundation Investment Committee; Member, Miami University Board of Visitors (2008-2011); Trustee of Victory Funds (2005-2008) and Chairman, Investment Committee (2007-2008); Member, Service Provider Committee (2005-2008) and Director of Best Transport (2006-2019).
Dr. Manuel H. Johnson c/o Johnson Smick International, Inc. 220 I Street, NE — Suite 200 Washington, D.C. 20002 Birth Year 1949	Trustee	Since July 1991	Senior Partner, Johnson Smick International, Inc. (consulting firm); Chairperson of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since July 1991); Co-Chairman and a founder of the Group of Seven Council (G7C) (international economic commission); formerly, Chairperson of the Audit Committee (July 1991-September 2006), Vice Chairman of the Board of Governors of the Federal Reserve System and Assistant Secretary of the U.S. Treasury.	86	Director of NVR, Inc. (home construction).
Joseph J. Kearns c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1942	Trustee	Since August 1994	Senior Adviser, Kearns & Associates LLC (investment consulting); Chairperson of the Audit Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 1994); Director, Rubicorn Investments (since February 2019); formerly, Deputy Chairperson of the Audit Committee (July 2003-September 2006) and Chairperson of the Audit Committee of various Morgan Stanley Funds (since August 1994); CFO of the J. Paul Getty Trust (1982-1999).	87	Prior to August 10, 2016, Director of Electro Rent Corporation (equipment leasing); Prior to December 31, 2013, Director of The Ford Family Foundation.

32

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Address and Birth Year of Independent Trustee	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years and Other Relevant Professional Experience	Number of Funds in Fund Complex Overseen by Independent Trustee**	Other Directorships Held by Independent Trustee***
Michael F. Klein c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1958	Trustee	Since August 2006	Managing Director, Aetos Alternatives Management, LP (since March 2000); Co-President, Aetos Alternatives Management, LP (since January 2004) and Co-Chief Executive Officer of Aetos Alternatives Management, LP (since August 2013); Chairperson of the Fixed Income Sub-Committee of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 2006); formerly, Managing Director, Morgan Stanley & Co. Inc. and Morgan Stanley Dean Witter Investment Management and President, various Morgan Stanley Funds (June 1998-March 2000); Principal, Morgan Stanley & Co. Inc. and Morgan Stanley Dean Witter Investment Management (August 1997-December 1999).	86	Director of certain investment funds managed or sponsored by Aetos Alternatives Management, LP; Director of Sanitized AG and Sanitized Marketing AG (specialty chemicals).
Patricia Maleski c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1960	Trustee	Since January 2017	Managing Director, JPMorgan Asset Management (2004-2016); Oversight and Control Head of Fiduciary and Conflicts of Interest Program (2015-2016); Chief Control Officer-Global Asset Management (2013-2015); President, JPMorgan Funds (2010-2013); Chief Administrative Officer (2004-2013); various other positions including Treasurer and Board Liaison (since 2001).	87	None.
W. Allen Reed c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1947	Chair of the Board and Trustee	Chair of the Boards since August 2020 and Trustee since August 2006	Chair of the Boards of various Morgan Stanley Funds (since August 2020); Chairperson of the Governance Committee; Chairperson of the Equity Sub-Committee of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 2006); formerly, Vice Chair of the Boards of various Morgan Stanley Funds (January 2020-August 2020); President and Chief Executive Officer of General Motors Asset Management; Chairman and Chief Executive Officer of the GM Trust Bank and Corporate Vice President of General Motors Corporation (August 1994-December 2005).	86	Formerly, Director of Legg Mason, Inc. (2006-2019); and Director of the Auburn University Foundation (2010-2015).

*  This is the earliest date the Trustee began serving the Morgan Stanley Funds. Each Trustee serves an indefinite term, until his or her successor is elected.

**  The Fund Complex includes (as of December 31, 2019) all open-end and closed-end funds (including all of their portfolios) advised by Morgan Stanley Investment Management Inc. (the "Adviser") and any funds that have an adviser that is an affiliated person of the Adviser (including, but not limited to, Morgan Stanley AIP GP LP).

***  This includes any directorships at public companies and registered investment companies held by the Trustee at any time during the past five years.

33

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited) (cont'd)

Executive Officers:

Name, Address and Birth Year of Executive Officer	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years
John H. Gernon 522 Fifth Avenue New York, NY 10036 Birth Year 1963	President and Principal Executive Officer	Since September 2013	President and Principal Executive Officer of the Equity and Fixed Income Funds and the Morgan Stanley AIP Funds (since September 2013) and the Liquidity Funds and various money market funds (since May 2014) in the Fund Complex; Managing Director of the Adviser; Head of Public Markets Product Development (since 2006).
Timothy J. Knierim 522 Fifth Avenue New York, NY 10036 Birth Year 1959	Chief Compliance Officer	Since December 2016	Managing Director of the Adviser and various entities affiliated with the Adviser; Chief Compliance Officer of various Morgan Stanley Funds and the Adviser (since December 2016) and Chief Compliance Officer of Morgan Stanley AIP GP LP (since 2014). Formerly, Managing Director and Deputy Chief Compliance Officer of the Adviser (2014-2016); and formerly, Chief Compliance Officer of Prudential Investment Management, Inc. (2007-2014).
Francis J. Smith 522 Fifth Avenue New York, NY 10036 Birth Year 1965	Treasurer and Principal Financial Officer	Treasurer since July 2003 and Principal Financial Officer since September 2002	Managing Director of the Adviser and various entities affiliated with the Adviser; Treasurer (since July 2003) and Principal Financial Officer of various Morgan Stanley Funds (since September 2002).
Mary E. Mullin 522 Fifth Avenue New York, NY 10036 Birth Year 1967	Secretary	Since June 1999	Managing Director of the Adviser; Secretary of various Morgan Stanley Funds (since June 1999).
Michael J. Key 522 Fifth Avenue New York, NY 10036 Birth Year 1979	Vice President	Since June 2017	Vice President of the Equity and Fixed Income Funds, Liquidity Funds, various money market funds and the Morgan Stanley AIP Funds in the Fund Complex (since June 2017); Executive Director of the Adviser; Head of Product Development for Equity and Fixed Income Funds (since August 2013).

*  This is the earliest date the officer began serving the Morgan Stanley Funds. Each officer serves a one-year term, until his or her successor is elected and qualifies.

34

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Adviser and Administrator

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

Distributor

Morgan Stanley Distribution, Inc.
522 Fifth Avenue
New York, New York 10036

Dividend Disbursing and Transfer Agent

DST Asset Manager Solutions, Inc.
2000 Crown Colony Drive
Quincy, Massachusetts 02169

Co-Transfer Agent

Morgan Stanley Services Company, Inc.
522 Fifth Avenue
New York, New York 10036

Custodian

State Street Bank and Trust Company
One Lincoln Street
Boston, Massachusetts 02111

Legal Counsel

Dechert LLP
1095 Avenue of the Americas
New York, New York 10036

Counsel to the Independent Trustees

Perkins Coie LLP
1155 Avenue of the Americas,
22nd Floor
New York, New York 10036

Independent Registered Public Accounting Firm

Ernst & Young LLP
200 Clarendon Street
Boston, Massachusetts 02116

Reporting to Shareholders

Each Morgan Stanley fund provides a complete schedule of portfolio holdings in its Semi-Annual and the Annual Reports within 60 days of the end of the fund's second and fourth fiscal quarters. The Semi-Annual and Annual Reports are filed electronically with the Securities and Exchange Commission ("SEC") on Form N-CSRS and Form N-CSR, respectively. Morgan Stanley also delivers the Semi-Annual and Annual Reports to fund shareholders and makes these reports available on its public website, www.morganstanley.com/im/shareholderreports. Each Morgan Stanley non-money market fund also files a complete schedule of portfolio holdings with the SEC for the fund's first and third fiscal quarters as an attachment to Form N-PORT. Morgan Stanley does not deliver the reports for the first and third fiscal quarters to shareholders, nor are the reports posted to the Morgan Stanley public website. However, the holdings for each money market fund are posted to the Morgan Stanley public website. You may obtain the Form N-PORT filings (as well as the Form N-CSR and N-CSRS filings) by accessing the SEC's website, www.sec.gov. You can also request copies of these materials, upon payment of a duplicating fee, by electronic request at the SEC's email address (publicinfo@sec.gov).

Proxy Voting Policies and Procedures and Proxy Voting Record

You may obtain a copy of the Trust's Proxy Voting Policy and Procedures and information regarding how the Trust voted proxies relating to portfolio securities during the most recent twelve-month period ended June 30, without charge, upon request, by calling toll free 1 (800) 548-7786 or by visiting our website at www.morganstanley.com/im/shareholderreports. This information is also available on the SEC's website at www.sec.gov.

This report is authorized for distribution only when preceded or accompanied by a prospectus or summary prospectus of the applicable Fund of Morgan Stanley Institutional Fund Trust, which describes in detail the Fund's investment policies, risks, fees and expenses. Please read the prospectus carefully before you invest or send money. For additional information, including information regarding the investments comprising the Fund, please visit our website at www.morganstanley.com/im/shareholderreports or call toll free 1 (800) 548-7786.

35

Printed in U.S.A.
This Report has been prepared for shareholders and may be distributed to others only if preceded or accompanied by a current prospectus.

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

© 2020 Morgan Stanley. Morgan Stanley Distribution, Inc.

IFTSLANN
3298773 EXP 11.30.21

INVESTMENT MANAGEMENT

Morgan Stanley Institutional Fund Trust

Short Duration Income Portfolio

Annual Report

September 30, 2020

Beginning on January 1, 2021, as permitted by regulations adopted by the Securities and Exchange Commission ("SEC"), paper copies of the Fund's Annual and Semi-Annual Reports to Shareholders ("Shareholder Reports") will no longer be sent by mail, unless you specifically request paper copies of the Shareholder Reports from the Fund or from your financial intermediary, such as a broker-dealer or a bank. Instead, the Shareholder Reports will be made available on the Fund's website, https://www.morganstanley.com/im/shareholderreports and you will be notified by mail each time a Shareholder Report is posted and provided with a website link to access the Shareholder Report. If you already elected to receive Shareholder Reports electronically, you will not be affected by this change and you need not take any action. You may elect to receive Shareholder Reports and other communications from the Fund electronically anytime by contacting your financial intermediary or, if you are a direct investor, please follow the instructions on the envelope.

Beginning on January 1, 2019, you may elect to receive all future Shareholder Reports in paper free of charge. If you invest through a financial intermediary, you can contact your financial intermediary to request that you continue to receive paper copies of your Shareholder Reports. If you invest directly with the Fund, please follow the instructions on the envelope to let the Fund know you wish to continue receiving paper copies of your Shareholder Reports. Your election to receive Shareholder Reports in paper will apply to all funds held in your account if you invest through your financial intermediary or all funds held with the fund complex if you invest directly with a fund.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Table of Contents

Shareholders' Letter	2
Expense Example	3
Investment Overview	4
Portfolio of Investments	7
Statement of Assets and Liabilities	15
Statement of Operations	17
Statements of Changes in Net Assets	18
Financial Highlights	20
Notes to Financial Statements	25
Report of Independent Registered Public Accounting Firm	33
Investment Advisory Agreement Approval	34
Liquidity Risk Management Program	36
Privacy Notice	37
Trustee and Officer Information	39

This report is authorized for distribution only when preceded or accompanied by a prospectus or summary prospectus of the applicable Fund of the Morgan Stanley Institutional Fund Trust. To receive a prospectus and/or statement of additional information ("SAI"), which contains more complete information such as investment objectives, charges, expenses, policies for voting proxies, risk considerations and describes in detail each of the Fund's investment policies to the prospective investor, please call toll free 1 (800) 548-7786. Please read the prospectuses carefully before you invest or send money.

Additionally, you can access information about the Fund, including performance, characteristics and investment team commentary, through Morgan Stanley Investment Management's website: www.morganstanley.com/im/shareholderreports.

Market forecasts provided in this report may not necessarily come to pass. There is no guarantee that any sectors mentioned will continue to perform as discussed herein or that securities in such sectors will be held by the Fund in the future. There is no assurance that a fund will achieve its investment objective. Funds are subject to market risk, which is the possibility that market values of securities owned by the Fund will decline and, therefore, the value of the Fund's shares may be less than what you paid for them. Accordingly, you can lose money investing in this Fund. Please see the prospectus for more complete information on investment risks.

1

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Shareholders' Letter (unaudited)

Dear Shareholders,

We are pleased to provide this Annual Report, in which you will learn how your investment in Short Duration Income Portfolio (the "Fund") performed during the latest twelve-month period.

Morgan Stanley Investment Management is a client-centric, investor-led organization. Our global presence, intellectual capital, and breadth of products and services enable us to partner with investors to meet the evolving challenges of today's financial markets. We aim to deliver superior investment service and to empower our clients to make the informed decisions that help them reach their investment goals.

As always, we thank you for selecting Morgan Stanley Investment Management, and look forward to working with you in the months and years ahead.

Sincerely,

John H. Gernon
President and Principal Executive Officer

October 2020

2

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Expense Example (unaudited)

Short Duration Income Portfolio

As a shareholder of the Fund, you may incur two types of costs: (1) transactional costs, including sales charge (loads) on purchase payments; and (2) ongoing costs, which may include advisory fees, administration fees, distribution and shareholder services fees; and other Fund expenses. This example is intended to help you understand your ongoing costs (in dollars) of investing in the Fund and to compare these costs with the ongoing costs of investing in other mutual funds.

This example is based on an investment of $1,000 invested at the beginning of the six-month period ended September 30, 2020 and held for the entire six-month period.

Actual Expenses

The table below provides information about actual account values and actual expenses. You may use the information in this table, together with the amount you invested, to estimate the expenses that you paid over the period. Simply divide your account value by $1,000 (for example, an $8,600 account value divided by $1,000 = 8.6), then multiply the result by the number in the table under the heading entitled "Actual Expenses Paid During Period" to estimate the expenses you paid on your account during this period.

Hypothetical Example for Comparison Purposes

The table below provides information about hypothetical account values and hypothetical expenses based on the Fund's actual expense ratio and an assumed rate of return of 5% per year before expenses, which is not the Fund's actual return. The hypothetical account values and expenses may not be used to estimate the actual ending account balance or expenses you paid for the period. You may use this information to compare the ongoing costs of investing in the Fund and other funds. To do so, compare this 5% hypothetical example with the 5% hypothetical examples that appear in the shareholder reports of the other funds.

Please note that the expenses shown in the table are meant to highlight your ongoing costs only and do not reflect any transactional costs, such as sales charges (loads, if applicable). Therefore, the information for each class in the table is useful in comparing ongoing costs only, and will not help you determine the relative total costs of owning different funds. In addition, if these transactional costs were included, your costs would have been higher.

	Beginning Account Value 4/1/20		Actual Ending Account Value 9/30/20		Hypothetical Ending Account Value		Actual Expenses Paid During Period*		Hypothetical Expenses Paid During Period*		Net Expense Ratio During Period**
Short Duration Income Portfolio Class I	$	1,000.00	$	1,059.80	$	1,023.55	$	1.49	$	1.47		0.29	%
Short Duration Income Portfolio Class A		1,000.00		1,059.70		1,022.30		2.78		2.73		0.54
Short Duration Income Portfolio Class L		1,000.00		1,058.50		1,021.05		4.07		3.99		0.79
Short Duration Income Portfolio Class C		1,000.00		1,054.50		1,018.55		6.63		6.51		1.29
Short Duration Income Portfolio Class IS		1,000.00		1,061.40		1,023.75		1.29		1.26		0.25

*  Expenses are calculated using each Fund Class' annualized net expense ratio (as disclosed), multiplied by the average account value over the period and multiplied by 183/366 (to reflect the most recent one-half year period).

**  Annualized.

3

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Overview (unaudited)

Short Duration Income Portfolio

The Fund seeks above-average total return over a market cycle of three to five years.

Performance

For the fiscal year ended September 30, 2020, the Fund's Class I shares had a total return based on net asset value and reinvestment of distributions per share of 3.20%, net of fees. The Fund's Class I shares underperformed against the Fund's benchmark, the Bloomberg Barclays 1-3 Year U.S. Government/Credit Index (the "Index"), which returned 3.73%.

Factors Affecting Performance

•  Government bond yields have declined significantly over the period in the U.S. and throughout the world, following a downturn in the first quarter of 2020 due to the coronavirus. This helped absolute performance for the portfolio and benchmark, as the portfolio had similar duration to the index over the period.

•  The portfolio's overweight to investment grade corporate bonds contributed to relative performance as spreads have tightened significantly following the Federal Reserve's (Fed) intervention in the bond markets. In March 2020, rates were cut to the effective lower bound and trillions of dollars were injected into money markets and bond markets. New programs were begun with a whole new set of acronyms (TALF, MMCP, CPFF). These helped significantly calm markets, particularly government bond markets where yields had perversely rose significantly as virus and economic news got worse. By March 19, 2020, U.S. Treasury and other global government bond market yields began to fall, signaling success for the Fed's first objective, stabilizing money markets and lowering U.S. Treasury yields. Importantly, the rapid fall in U.S. Treasury yields allowed high quality corporate bond yields to fall as well, signaling help for the embattled private economy.

•  The portfolio's exposure to securitized credit (non-agency and agency residential mortgage-backed securities) also contributed to relative performance, particularly in the second quarter of 2020 as certain areas of the securitized credit markets rebounded faster than others. For example, the portfolio's exposure to asset-backed securities and non-agency commercial mortgage-backed securities was a main detractor from relative performance due to these

areas' lagged recovery following the market sell-off in the first quarter of 2020.

Management Strategies

•  We see little risk of government bond yields rising meaningfully anytime soon. Recent rises in yields during September 2020 appear to have been more technical in nature and/or related to shifting probabilities of who will be elected the next U.S. president. However, further declines in yields also seem unlikely, given that most central banks have now cut interest rates to as low as they feel comfortable doing. Nonetheless, further cuts and other policy innovations could still happen if there is a turn for the worse, so there is still a case, we believe, for owning high-quality government bonds as a hedge against further stress, even if much less than normal.

•  The perception that the Fed is likely to pursue an exceptionally easy monetary policy relative to others has caused a cheapening of the U.S. dollar. However, heightened global risk aversion in September 2020 caused the dollar to recover some. While we remain longer-term modest-dollar bears, we do not think there is enough clarity on relative economic performances and resolution of who will lead the U.S. to be highly confident the dollar will fall meaningfully in the near term.

•  We remain constructive on corporate credit. Although we continue to hold a positive and upbeat view with regard to the evolution of the economy and credit spreads, risks remain. Rising infection rates, leading to larger and more aggressive lockdowns, could easily slow economies and upend our views. We do not think this is likely, as all governments seem to be adopting more selective, targeted lockdowns to deal with local issues. As long as local issues do not spread and/or hospitalization rates/mortality rates do not climb too much, economies should be fine. Vaccines continue to be the linchpin of a broader solution to get sectors of the economy like travel, leisure and entertainment back to semi-normal, thus allowing national incomes to return back to pre-COVID-19 levels.

•  In the securitized assets sector, we still have a positive fundamental credit outlook for U.S. residential and consumer credit conditions given various government support programs that have been put in place in response to the coronavirus pandemic.

4

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Overview (unaudited) (cont'd)

Short Duration Income Portfolio

*  Minimum Investment

In accordance with SEC regulations, the Fund's performance shown assumes that all recurring fees (including management fees) were deducted and all dividends and distributions were reinvested. The performance of Class A, Class L, Class C and Class IS shares will vary from the performance of Class I shares based upon their different inception dates and will be negatively impacted by additional fees assessed to those classes (where applicable).

Performance Compared to the Bloomberg Barclays 1-3 Year U.S. Government/Credit Index⁽¹⁾, the Short Duration Income Blend Index⁽²⁾ and the Lipper Short Investment Grade Debt Funds Index⁽³⁾

	Period Ended September 30, 2020 Total Returns(4)
				Average Annual
	One Year			Five Years			Ten Years			Since Inception(10)
Fund — Class I Shares w/o sales charges(5)		3.20	%		3.71	%		2.57	%		3.11	%
Fund — Class A Shares w/o sales charges(6)		3.06			3.49			2.32			0.64
Fund — Class A Shares with maximum 2.00% sales charges(6)		0.98			3.06			2.11			0.48
Fund — Class L Shares w/o sales charges(7)		2.69			3.19			—			2.15
Fund — Class C Shares w/o sales charges(8)		2.16			2.66			—			2.28
Fund — Class C Shares with maximum 1.00% deferred sales charges(8)		1.16			2.66			—			2.28
Fund — Class IS Shares w/o sales charges(9)		3.37			—			—			4.02
Bloomberg Barclays 1-3 Year U.S. Government/Credit Index		3.73			2.09			1.57			3.92
Short Duration Income Blend Index		3.73			1.85			1.45			3.87
Lipper Short Investment Grade Debt Funds Index		3.86			2.51			2.04			3.76

Performance data quoted represents past performance, which is no guarantee of future results, and current performance may be lower or higher than the figures shown. Performance assumes that all dividends and distributions, if any, were reinvested. For the most recent month-end performance figures, please visit www.morganstanley.com/im/shareholderreports. Investment returns and principal value will fluctuate so that Fund shares, when redeemed, may be worth more or less than their original cost. Total returns do not reflect the deduction of taxes that a shareholder would pay on Fund distributions or the redemption of Fund shares. Performance of share classes will vary due to differences in sales charges and expenses.

⁽¹⁾  The Bloomberg Barclays 1-3 Year U.S. Government/Credit Index tracks the securities in the 1-3 year maturity range of the Bloomberg Barclays U.S. Government/Credit Index which tracks investment-grade (BBB-/Baa3) or higher publicly traded fixed rate U.S. government, U.S. agency, and corporate issues. The Index is unmanaged and its returns do not include any sales charges or fees. Such costs would lower performance. It is not possible to invest directly in an index.

5

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Overview (unaudited) (cont'd)

Short Duration Income Portfolio

⁽²⁾  The Short Duration Income Blend Index is a performance linked benchmark of the old benchmarks represented by Bloomberg Barclays 1-3 Year U.S. Government/Credit Index for periods from the Fund's inception to January 8, 2016, the ICE BofA 1-Year U.S. Treasury Note Index (benchmark that tracks one-year U.S. government securities) from January 9, 2016 to July 31, 2019 and the new benchmark represented by Bloomberg Barclays 1-3 Year U.S. Government/Credit index for periods thereafter. The Index is unmanaged and its returns do not include any sales charges or fees. Such costs would lower performance. It is not possible to invest directly in an index.

⁽³⁾  The Lipper Short Investment Grade Debt Funds Index is an equally weighted performance index of the largest qualifying funds (based on net assets) in the Lipper Short Investment Grade Debt Funds classification. The Index, which is adjusted for capital gains distributions and income dividends, is unmanaged and should not be considered an investment. There are currently 30 funds represented in this Index. As of the date of this report, the Fund was in the Lipper Short Investment Grade Debt Funds classification.

⁽⁴⁾  Total returns for the Fund reflect expenses waived and/or reimbursed, if applicable, by the Adviser. Without such waivers and/or reimbursements, total returns would have been lower.

⁽⁵⁾  Commenced operations on March 31, 1992.

⁽⁶⁾  Commenced offering on September 28, 2007.

⁽⁷⁾  Commenced offering on April 27, 2012.

⁽⁸⁾  Commenced offering on April 30, 2015.

⁽⁹⁾  Commenced offering on January 11, 2016.

⁽¹⁰⁾  For comparative purposes, average annual since inception returns listed for the Indexes refer to the inception date of Class I of the Fund, not the inception of the Indexes.

6

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments

Short Duration Income Portfolio

	Face Amount (000)			Value (000)
Fixed Income Securities (92.6%)
Agency Adjustable Rate Mortgages (0.2%)
Federal Home Loan Mortgage Corporation, Conventional Pools: 1 Year CMT + 2.31%, 3.46%, 3/1/37	$	277		$	294
1 Year CMT + 2.18%, 3.60%, 6/1/38		136			143
1 Year CMT + 2.32%, 3.61%, 7/1/38		218			231
1 Year CMT + 2.33%, 3.80%, 1/1/36		223			236
					904
Agency Bond — Consumer Discretionary (U.S. Government Guaranteed) (0.1%)
Safina Ltd.
2.00%, 12/30/23		290			297
Agency Fixed Rate Mortgages (0.3%)
Federal Home Loan Mortgage Corporation, Gold Pools:
4.50%, 12/1/24		155			164
6.50%, 4/1/24		—	@		1
7.50%, 5/1/35		18			22
8.00%, 8/1/32		11			13
8.50%, 8/1/31		11			13
Federal National Mortgage Association, Conventional Pools:
4.50%, 6/1/24 — 7/1/24		261			275
5.00%, 12/1/23 — 12/1/24		125			132
6.00%, 9/1/37		46			54
6.50%, 2/1/28 — 10/1/32		152			171
7.00%, 7/1/29 — 3/1/37		177			203
7.50%, 8/1/37		23			29
8.00%, 4/1/33		43			53
8.50%, 10/1/32		20			25
Government National Mortgage Association, Various Pools:
6.00%, 11/15/38		80			92
8.50%, 7/15/30		26			28
					1,275
Asset-Backed Securities (13.2%)
Ajax Mortgage Loan Trust
1.70%, 5/25/59 (a)		812			814
Ally Auto Receivables Trust
1.75%, 12/15/21		37			37
AMSR Trust
2.11%, 9/17/37 (a)		975			979
Aqua Finance Trust
3.14%, 7/16/40 (a)		346			354
Avant Loans Funding Trust
4.11%, 7/15/22 (a)		211			211
Bayview Opportunity Master Fund Trust
3.50%, 1/28/55 (a)(b)		181			185
CarMax Auto Owner Trust,
1.70%, 11/15/24		1,800			1,843
1.98%, 11/15/21		—	@		—	@

	Face Amount (000)		Value (000)
Cascade Funding Mortgage Trust 3.40%, 4/25/30 (a)(b)	$	665	$	675
CFMT 2020-HB3 LLC
5.11%, 5/25/30 (a)(b)		800		808
CNH Equipment Trust
2.01%, 12/16/24		1,528		1,570
Consumer Loan Underlying Bond Credit Trust,
3.28%, 7/15/26 (a)		845		847
4.07%, 7/15/25 (a)		260		261
Fair Square Issuance Trust
2.90%, 9/20/24 (a)		300		300
Falcon Aerospace Ltd.
3.60%, 9/15/39 (a)		401		370
FCI Funding 2019-1 LLC
3.63%, 2/18/31 (a)		229		233
Finance of America HECM Buyout
2.01%, 2/25/30 (a)(b)		1,309		1,309
Foundation Finance Trust,
3.30%, 7/15/33 (a)		194		197
3.86%, 11/15/34 (a)		370		382
FREED ABS Trust,
3.19%, 11/18/26 (a)		900		894
3.87%, 6/18/26 (a)		500		501
4.61%, 10/20/25 (a)		560		562
GAIA Aviation Ltd.
3.97%, 12/15/44 (a)		582		518
GM Financial Automobile Leasing Trust
1.67%, 12/20/22		830		843
GM Financial Automobile Leasing Trust 2020-2
0.80%, 7/20/23		220		222
GM Financial Consumer Automobile Receivables Trust
2.81%, 12/16/22		837		848
Hyundai Auto Lease Securitization Trust
2.92%, 7/15/21 (a)		108		108
Hyundai Auto Receivables Trust
1.77%, 1/18/22		79		79
Kubota Credit Owner Trust
0.59%, 10/15/24 (a)		675		678
LL ABS Trust
2.33%, 1/17/28 (a)		700		700
Lunar Aircraft Ltd.
3.38%, 2/15/45 (a)		182		170
MACH 1 Cayman Ltd.
3.47%, 10/15/39 (a)		511		470
Mercedes-Benz Auto Receivables Trust
0.55%, 2/18/25		330		332
MFA LLC,
3.35%, 11/25/47 (a)		358		359
3.88%, 5/25/48 (a)		510		510
4.16%, 7/25/48 (a)		358		359
Mosaic Solar Loan Trust
2.10%, 4/20/46 (a)		380		390

The accompanying notes are an integral part of the financial statements.
7

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Short Duration Income Portfolio

	Face Amount (000)		Value (000)
Asset-Backed Securities (cont'd)
Nationstar HECM Loan Trust, 1.27%, 9/25/30 (a)(b)	$	900	$	900
2.27%, 11/25/29 (a)(b)		122		123
New Residential Advance Receivables Trust
1.43%, 8/15/53 (a)		1,170		1,173
2.80%, 10/15/51 (a)		352		352
Nissan Auto Receivables Owner Trust
1.75%, 10/15/21		87		87
North Carolina State Education Assistance Authority
3 Month USD LIBOR + 0.80%, 1.04%, 7/25/25 (b)		69		69
NRZ Advance Receivables Trust
1.48%, 9/15/53 (a)		1,380		1,385
NRZ Excess Spread-Collateralized Notes,
4.37%, 1/25/23 (a)		237		234
4.59%, 2/25/23 (a)		352		340
NYCTL Trust
2.19%, 11/10/32 (a)		580		588
Ocwen Master Advance Receivables Trust
1.28%, 8/15/52 (a)		1,150		1,156
OnDeck Asset Securitization Trust II LLC
3.33%, 11/18/24 (a)		900		816
Option One Mortgage Loan Trust Asset-Backed Certificates
1 Month USD LIBOR + 0.50%, 0.66%, 8/20/30 (b)		86		85
Oscar US Funding X LLC
3.18%, 5/10/23 (a)		830		851
Oscar US Funding XI LLC
2.49%, 8/10/22 (a)		170		171
Oxford Finance Funding LLC
3.10%, 2/15/28 (a)		350		356
PFS Financing Corp.,
1.27%, 6/15/25 (a)		1,500		1,515
2.23%, 10/15/24 (a)		1,160		1,194
2.74%, 10/17/22 (a)		440		439
2.86%, 4/15/24 (a)		230		236
2.89%, 2/15/23 (a)		275		278
3.19%, 4/17/23 (a)		300		304
3.52%, 10/15/23 (a)		162		167
Pretium Mortgage Credit Partners I LLC
2.86%, 5/27/59 (a)		699		697
Prosper Marketplace Issuance Trust,
3.59%, 7/15/25 (a)		700		705
3.96%, 10/15/24 (a)		97		97
PRPM LLC,
3.75%, 4/25/23 (a)(b)		235		238
3.97%, 4/25/24 (a)		616		622
Raptor Aircraft Finance I LLC
4.21%, 8/23/44 (a)		807		722
RCO V Mortgage LLC,
3.47%, 11/25/24 (a)		774		774
4.46%, 10/25/23 (a)		1		1

	Face Amount (000)		Value (000)
ReadyCap Lending Small Business Loan Trust, Daily U.S. Prime Rate – 0.50%, 2.75%, 12/27/44 (a)(b)	$	249	$	232
Republic FInance Issuance Trust
3.43%, 11/22/27 (a)		800		814
Santander Retail Auto Lease Trust
1.74%, 7/20/23 (a)		1,330		1,358
SFS Asset Securitization LLC
4.24%, 6/10/25 (a)		814		813
Small Business Lending Trust
2.85%, 7/15/26 (a)		138		136
Sofi Consumer Loan Program Trust,
3.14%, 2/25/27 (a)		110		111
3.35%, 4/26/27 (a)		98		99
3.67%, 8/25/27 (a)		353		357
SPS Servicer Advance Receivables Trust Advance Receivables Backed Notes
2.77%, 10/15/52 (a)		325		322
TLF National Tax Lien Trust
3.09%, 12/15/29 (a)		277		278
Towd Point Mortgage Trust,
1 Month USD LIBOR + 0.60%, 0.75%, 2/25/57 (a)(b)		248		248
2.75%, 4/25/57 (a)(b)		83		86
Upgrade Receivables Trust,
4.09%, 3/15/25 (a)		218		218
4.53%, 11/15/24 (a)		131		131
Upstart Securitization Trust
3.73%, 9/20/29 (a)		850		848
VCAT LLC
3.67%, 8/25/50 (a)		981		983
Vericrest Opportunity Loan Trust,
2.98%, 2/25/50 (a)		776		777
3.18%, 10/25/49 (a)		392		393
3.35%, 9/25/49 (a)		601		603
Verizon Owner Trust,
1 Month USD LIBOR + 0.27%, 0.43%, 4/20/22 (a)(b)		19		19
0.47%, 2/20/25		950		952
2.93%, 9/20/23		600		615
Volkswagen Auto Lease Trust
1.99%, 11/21/22		1,280		1,305
VOLT LXXX LLC
3.23%, 10/25/49 (a)		412		413
VOLT LXXXIII LLC
3.33%, 11/26/49 (a)		625		628
VOLT LXXXV LLC
3.23%, 1/25/50 (a)		440		442
VOLT LXXXVIII LLC
2.98%, 3/25/50 (a)		642		642
				50,416

The accompanying notes are an integral part of the financial statements.
8

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Short Duration Income Portfolio

	Face Amount (000)		Value (000)
Collateralized Mortgage Obligations — Agency Collateral Series (0.3%)
Federal Home Loan Mortgage Corporation, REMIC 7.50%, 9/15/29	$	319	$	375
Government National Mortgage Association, REMIC
1 Month USD LIBOR + 0.50%, 0.65%, 3/20/61 (b)		118		118
1 Month USD LIBOR + 0.56%, 0.71%, 9/20/62 (b)		528		530
				1,023
Commercial Mortgage-Backed Securities (1.2%)
CSMC Trust
3.53%, 8/15/37 (a)		575		597
CSWF 2018-TOP
1 Month USD LIBOR + 1.45%, 1.60%, 8/15/35 (a)(b)		640		612
Federal Home Loan Mortgage Corporation
3.03%, 10/25/20 (b)		1		1
HPLY Trust
1 Month USD LIBOR + 2.35%, 2.50%, 11/15/36 (a)(b) cBBerg.mtg_reset_slope: 1.00		410		379
Hudsons Bay Simon JV Trust
1 Month USD LIBOR + 1.83%, 1.99%, 8/5/34 (a)(b)		185		171
JP Morgan Chase Commercial Mortgage Securities Corp.
4.13%, 7/5/31 (a)		1,100		1,173
Natixis Commercial Mortgage Securities Trust
1 Month USD LIBOR + 2.20%, 2.35%, 7/15/36 (a)(b)		850		819
VMC Finance 2019-FL3 LLC
1 Month USD LIBOR + 2.05%, 2.20%, 9/15/36 (a)(b)		733		709
				4,461
Corporate Bonds (70.0%)
Energy (0.1%)
Midwest Connector Capital Co. LLC
3.63%, 4/1/22 (a)		475		478
Finance (31.7%)
ABN Amro Bank N.V.
3.40%, 8/27/21 (a)		650		668
AerCap Ireland Capital DAC/AerCap Global Aviation Trust
3.30%, 1/23/23		1,260		1,265
Air Lease Corp.
2.63%, 7/1/22		1,440		1,460
American Express Co.,
3.00%, 2/22/21		700		706
3.38%, 5/17/21		1,050		1,067
3.70%, 11/5/21		665		687
American International Group, Inc.
4.88%, 6/1/22		2,200		2,359
American Tower Corp.
2.40%, 3/15/25		600		635

	Face Amount (000)		Value (000)
Anthem, Inc. 3.50%, 8/15/24	$	1,200	$	1,317
ANZ New Zealand International Ltd.
1.90%, 2/13/23 (a)		1,510		1,556
Aon Corp.
2.20%, 11/15/22		575		595
Avolon Holdings Funding Ltd.
2.88%, 2/15/25 (a)		625		574
Banco Bilbao Vizcaya Argentaria SA
0.88%, 9/18/23		1,600		1,600
Banco Santander Chile
2.70%, 1/10/25 (a)		800		845
Bank of America Corp.,
3.88%, 8/1/25		1,700		1,935
4.13%, 1/22/24		2,000		2,217
MTN
3.30%, 1/11/23		1,220		1,296
Bank of Montreal
2.90%, 3/26/22		1,030		1,069
Bank of New York Mellon Corp. (The)
2.20%, 8/16/23		1,400		1,469
Bank of Nova Scotia (The),
1.63%, 5/1/23		1,600		1,643
2.00%, 11/15/22		1,175		1,214
Banque Federative du Credit Mutuel SA
2.38%, 11/21/24 (a)		1,350		1,429
Barclays PLC
4.61%, 2/15/23		1,200		1,256
BBVA USA
3.50%, 6/11/21		925		942
BNP Paribas SA
3.50%, 3/1/23 (a)		1,250		1,326
BPCE SA,
2.38%, 1/14/25 (a)		625		650
4.00%, 9/12/23 (a)		1,200		1,305
Canadian Imperial Bank of Commerce
2.25%, 1/28/25		1,130		1,194
Capital One Financial Corp.
3.20%, 1/30/23		2,500		2,641
Cigna Corp.
3.75%, 7/15/23		1,213		1,316
Citigroup, Inc.,
3.30%, 4/27/25		2,000		2,200
3.35%, 4/24/25		1,540		1,668
3.88%, 10/25/23		2,400		2,632
Citizens Bank NA
3.25%, 2/14/22		575		596
Cooperatieve Rabobank UA
3.95%, 11/9/22		1,340		1,425
Credit Suisse AG,
1.00%, 5/5/23		2,360		2,386
3.00%, 10/29/21		1,140		1,172

The accompanying notes are an integral part of the financial statements.
9

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Short Duration Income Portfolio

	Face Amount (000)		Value (000)
Finance (cont'd)
DBS Group Holdings Ltd. 2.85%, 4/16/22 (a)	$	360	$	372
Deutsche Bank AG
4.25%, 2/4/21		650		657
Equitable Financial Life Global Funding
1.40%, 7/7/25 (a)		1,000		1,022
Goldman Sachs Group, Inc. (The),
3.50%, 1/23/25 — 4/1/25		2,950		3,249
3.63%, 1/22/23		1,275		1,364
Guardian Life Global Funding
2.90%, 5/6/24 (a)		1,200		1,294
HSBC Holdings PLC
3.95%, 5/18/24		2,240		2,397
Intercontinental Exchange, Inc.
0.70%, 6/15/23		1,420		1,425
JPMorgan Chase & Co.,
3.13%, 1/23/25		1,550		1,692
3.63%, 5/13/24		1,170		1,293
4.02%, 12/5/24		2,660		2,921
KeyBank NA
2.30%, 9/14/22		475		493
LeasePlan Corp.
2.88%, 10/24/24 (a)		1,275		1,317
Lloyds Banking Group PLC
1.33%, 6/15/23		2,575		2,591
Macquarie Bank Ltd.,
2.10%, 10/17/22 (a)		1,500		1,549
2.30%, 1/22/25 (a)		1,075		1,140
Metropolitan Life Global Funding I,
0.90%, 6/8/23 (a)		1,140		1,153
0.95%, 7/2/25 (a)		1,275		1,287
1.95%, 9/15/21 — 1/13/23 (a)		2,210		2,263
National Australia Bank Ltd.
1.88%, 12/13/22		950		982
National Bank of Canada,
0.90%, 8/15/23		1,810		1,818
2.10%, 2/1/23		1,485		1,536
National Securities Clearing Corp.
1.20%, 4/23/23 (a)		710		723
Nationwide Building Society,
2.00%, 1/27/23 (a)		2,030		2,090
3.62%, 4/26/23 (a)		1,600		1,663
New York Life Global Funding,
1.10%, 5/5/23 (a)		1,030		1,048
2.25%, 7/12/22 (a)		470		486
2.95%, 1/28/21 (a)		350		353
NongHyup Bank
1.25%, 7/20/25 (a)		690		697
Nordea Bank Abp
1.00%, 6/9/23 (a)		1,450		1,471
PACCAR Financial Corp.
2.65%, 5/10/22		1,175		1,218

	Face Amount (000)		Value (000)
People's United Financial, Inc. 3.65%, 12/6/22	$	1,660	$	1,754
Protective Life Global Funding,
2.70%, 11/25/20 (a)		525		527
3.10%, 4/15/24 (a)		1,225		1,323
Royal Bank of Canada
2.55%, 7/16/24		1,275		1,365
Santander UK Group Holdings PLC
4.80%, 11/15/24		1,200		1,323
Santander UK PLC
2.10%, 1/13/23		1,100		1,136
Skandinaviska Enskilda Banken AB,
2.20%, 12/12/22 (a)		700		725
3.05%, 3/25/22 (a)		1,230		1,277
Societe Generale SA
2.63%, 1/22/25 (a)		1,175		1,213
Standard Chartered PLC
2.74%, 9/10/22 (a)		1,775		1,804
Sumitomo Mitsui Financial Group, Inc.
2.35%, 1/15/25		3,360		3,543
Sumitomo Mitsui Trust Bank Ltd.
0.80%, 9/12/23 (a)		2,350		2,355
Suncorp-Metway Ltd.
2.38%, 11/9/20 (a)		670		671
Synchrony Financial
4.25%, 8/15/24		625		679
TD Ameritrade Holding Corp.
3.75%, 4/1/24		1,225		1,352
Truist Bank,
2.15%, 12/6/24		1,525		1,617
2.80%, 5/17/22		550		572
UBS AG
2.45%, 12/1/20 (a)		600		601
United Overseas Bank Ltd.
3.20%, 4/23/21 (a)		340		345
Wells Fargo & Co.,
1.65%, 6/2/24		650		663
3.07%, 1/24/23		1,900		1,960
Westpac Banking Corp.
2.00%, 1/13/23		680		705
				121,389
Industrials (33.7%)
AbbVie, Inc.
2.60%, 11/21/24 (a)		3,660		3,881
Alibaba Group Holding Ltd.
2.80%, 6/6/23		1,275		1,345
Alimentation Couche-Tard, Inc.
2.70%, 7/26/22 (a)		800		826
Altria Group, Inc.,
2.35%, 5/6/25		1,500		1,587
3.49%, 2/14/22		375		390
American Honda Finance Corp.
1.00%, 9/10/25		1,200		1,201

The accompanying notes are an integral part of the financial statements.
10

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Short Duration Income Portfolio

	Face Amount (000)		Value (000)
Industrials (cont'd)
Amgen, Inc. 1.90%, 2/21/25	$	1,350	$	1,417
Amphenol Corp.
2.05%, 3/1/25		1,250		1,314
Anheuser-Busch InBev Worldwide, Inc.
4.15%, 1/23/25		2,340		2,650
Apple, Inc.
0.75%, 5/11/23		990		1,001
AT&T, Inc.
3.80%, 3/1/24		2,450		2,692
BAT International Finance PLC
3.25%, 6/7/22 (a)		2,000		2,085
Bayer US Finance II LLC
3.50%, 6/25/21 (a)		330		337
Bayer US Finance LLC
3.38%, 10/8/24 (a)		1,000		1,089
BMW US Capital LLC,
2.95%, 4/14/22 (a)		770		798
3.45%, 4/12/23 (a)		1,471		1,571
Boeing Co. (The)
4.51%, 5/1/23		1,660		1,752
BP Capital Markets America, Inc.
3.19%, 4/6/25		2,565		2,824
Bristol-Myers Squibb Co.
3.25%, 2/20/23		275		293
Canadian Natural Resources Ltd.
2.95%, 1/15/23		1,250		1,301
Caterpillar Financial Services Corp.
3.30%, 6/9/24		2,430		2,658
CC Holdings GS V LLC/Crown Castle GS III Corp.
3.85%, 4/15/23		1,225		1,320
Charter Communications Operating LLC/Charter Communications Operating Capital
4.91%, 7/23/25		850		984
Chevron Corp.
1.55%, 5/11/25		1,900		1,971
Crown Castle International Corp.
5.25%, 1/15/23		1,175		1,294
Cummins, Inc.
0.75%, 9/1/25		1,500		1,506
Daimler Finance North America LLC,
2.55%, 8/15/22 (a)		1,210		1,248
2.85%, 1/6/22 (a)		1,110		1,140
3.35%, 2/22/23 (a)		520		551
3.75%, 11/5/21 (a)		295		305
Dell International LLC/EMC Corp.
4.42%, 6/15/21 (a)		158		162
Deutsche Telekom International Finance BV
1.95%, 9/19/21 (a)		1,260		1,274
Diageo Capital PLC
2.13%, 10/24/24		1,350		1,433

	Face Amount (000)		Value (000)
DR Horton, Inc. 2.55%, 12/1/20	$	480	$	482
DuPont de Nemours, Inc.
2.17%, 5/1/23		1,670		1,688
Eaton Corp.
2.75%, 11/2/22		2,235		2,344
Enbridge, Inc.
2.50%, 1/15/25		750		790
Enterprise Products Operating LLC,
2.80%, 2/15/21		780		787
3.90%, 2/15/24		1,200		1,310
Fortune Brands Home & Security, Inc.
4.00%, 9/21/23		1,150		1,258
Fox Corp.
4.03%, 1/25/24		1,200		1,322
General Motors Financial Co., Inc.
3.95%, 4/13/24		1,250		1,324
Georgia-Pacific LLC
1.75%, 9/30/25 (a)		1,410		1,471
Gilead Sciences, Inc.
0.75%, 9/29/23		2,210		2,215
Glencore Funding LLC,
3.00%, 10/27/22 (a)		1,275		1,321
4.13%, 3/12/24 (a)		1,225		1,329
HCA, Inc.
5.00%, 3/15/24		1,600		1,794
Hyundai Capital America,
1.25%, 9/18/23 (a)		1,380		1,378
2.38%, 2/10/23 (a)		590		606
2.85%, 11/1/22 (a)		800		828
3.95%, 2/1/22 (a)		1,270		1,318
Imperial Brands Finance PLC
3.13%, 7/26/24 (a)		2,015		2,133
International Business Machines Corp.,
2.85%, 5/13/22		1,800		1,875
3.00%, 5/15/24		1,175		1,274
John Deere Capital Corp.,
0.70%, 7/5/23		710		719
3.45%, 1/10/24		1,225		1,341
Keurig Dr Pepper, Inc.
3.55%, 5/25/21		930		949
Kinder Morgan, Inc.
5.00%, 2/15/21 (a)		1,170		1,185
Las Vegas Sands Corp.
3.20%, 8/8/24		1,250		1,265
Lockheed Martin Corp.
2.50%, 11/23/20		90		90
Lowe's Cos., Inc.
3.13%, 9/15/24		1,230		1,339
Mondelez International Holdings Netherlands BV,
2.13%, 9/19/22 (a)		1,160		1,198
2.25%, 9/19/24 (a)		950		1,000

The accompanying notes are an integral part of the financial statements.
11

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Short Duration Income Portfolio

	Face Amount (000)		Value (000)
Industrials (cont'd)
Mondelez International, Inc. 0.63%, 7/1/22	$	1,270	$	1,275
NetApp, Inc.
1.88%, 6/22/25		1,000		1,037
Nissan Motor Co. Ltd.
3.04%, 9/15/23 (a)		1,750		1,775
Northrop Grumman Corp.,
2.08%, 10/15/20		580		580
3.50%, 3/15/21		1,220		1,238
Nucor Corp.
2.00%, 6/1/25		975		1,019
NXP BV/NXP Funding LLC/NXP USA, Inc.
2.70%, 5/1/25 (a)		1,540		1,633
PACCAR Financial Corp.
0.80%, 6/8/23		380		383
PayPal Holdings, Inc.
2.40%, 10/1/24		1,300		1,379
PepsiCo,Inc.
0.75%, 5/1/23		630		637
Philip Morris International, Inc.,
1.13%, 5/1/23		550		559
2.63%, 3/6/23		1,700		1,786
Raytheon Technologies Corp.
2.80%, 3/15/22 (a)		1,275		1,315
Reckitt Benckiser Treasury Services PLC
2.38%, 6/24/22 (a)		1,620		1,669
Reynolds American, Inc.
4.00%, 6/12/22		1,625		1,713
Roper Technologies, Inc.
1.00%, 9/15/25		950		953
Royalty Pharma PLC
1.20%, 9/2/25 (a)		1,475		1,472
Sabine Pass Liquefaction LLC
5.63%, 4/15/23		1,320		1,447
Schlumberger Finance Canada Ltd.
2.20%, 11/20/20 (a)		410		411
Seven & i Holdings Co., Ltd.
3.35%, 9/17/21 (a)		1,750		1,794
Siemens Financieringsmaatschappij N.V.
3.25%, 5/27/25 (a)		1,500		1,668
Sky Ltd.
3.75%, 9/16/24 (a)		2,330		2,602
Starbucks Corp.
2.10%, 2/4/21		2,080		2,090
Takeda Pharmaceutical Co. Ltd.
4.00%, 11/26/21		725		753
Takeda Pharmaceutical Co., Ltd.
4.40%, 11/26/23		1,775		1,973
Toyota Motor Credit Corp.,
0.50%, 8/14/23		1,490		1,494
1.15%, 5/26/22		1,260		1,276
2.90%, 3/30/23		1,300		1,379

	Face Amount (000)		Value (000)
TSMC Global Ltd. 0.75%, 9/28/25 (a)	$	1,575	$	1,562
Union Pacific Corp.
3.50%, 6/8/23		1,225		1,321
Volkswagen Group of America Finance LLC,
2.70%, 9/26/22 (a)		1,420		1,473
3.88%, 11/13/20 (a)		755		758
Walt Disney Co. (The)
1.75%, 8/30/24		1,225		1,276
Williams Cos., Inc. (The)
4.30%, 3/4/24		1,330		1,456
				129,289
Utilities (4.5%)
Ameren Corp.
2.50%, 9/15/24		2,510		2,662
CenterPoint Energy, Inc.
2.50%, 9/1/24		1,500		1,597
DTE Energy Co.
0.55%, 11/1/22		1,710		1,710
DTE Energy Co.
2.25%, 11/1/22		1,800		1,862
Enel Finance International N.V.
4.63%, 9/14/25 (a)		1,380		1,596
FirstEnergy Corp.
2.05%, 3/1/25		625		636
NextEra Energy Capital Holdings, Inc.
2.40%, 9/1/21		1,550		1,580
NiSource, Inc.
0.95%, 8/15/25		1,550		1,551
Southern Co. (The)
2.95%, 7/1/23		1,260		1,341
WEC Energy Group, Inc.
0.55%, 9/15/23		2,840		2,847
				17,382
				268,538
Mortgages — Other (6.0%)
Bunker Hill Loan Depositary Trust
1.72%, 2/25/55 (a)(b)		869		880
Cascade Funding Mortgage Trust,
2.80%, 6/25/69 (a)(b)		650		652
4.00%, 10/25/68 (a)(b)		545		568
CFMT 2020-ABC1 LLC
1.94%, 9/25/50 (a)(b)		1,725		1,725
CHL Mortgage Pass-Through Trust
5.50%, 5/25/34		94		95
CIM Trust
3.00%, 4/25/57 (a)(b)		356		365
Federal Home Loan Mortgage Corporation
1 Month USD LIBOR + 1.20%, 1.35%, 10/25/29 (b)		51		51
FMC GMSR Issuer Trust
4.23%, 9/25/24 (a)(b)		900		883

The accompanying notes are an integral part of the financial statements.
12

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Short Duration Income Portfolio

	Face Amount (000)		Value (000)
Mortgages — Other (cont'd)
Galton Funding Mortgage Trust, 3.50%, 11/25/57 (a)(b)	$	177	$	179
4.00%, 2/25/59 (a)(b)		135		137
GCAT Trust
2.65%, 10/25/68 (a)(b)		471		491
Gosforth Funding PLC
3 Month USD LIBOR + 0.45%, 0.70%, 8/25/60 (a)(b)		178		178
Government National Mortgage Association,
1 Month USD LIBOR + 0.28%, 0.43%, 5/20/63 (b)		15		15
1 Month USD LIBOR + 0.45%, 0.60%, 5/20/62 (b)		2		2
1 Month USD LIBOR + 0.60%, 0.75%, 1/20/64 (b)		171		171
Headlands Residential LLC
3.97%, 6/25/24 (a)		200		202
Homeward Opportunities Fund Trust
3.23%, 8/25/25 (a)		1,200		1,203
Lanark Master Issuer PLC,
3 Month USD LIBOR + 0.42%, 0.68%, 12/22/69 (b)		450		450
3 Month USD LIBOR + 0.77%, 1.03%, 12/22/69 (a)(b)		358		359
2.28%, 12/22/69 (a)(b)		360		367
LHOME Mortgage Trust
3.23%, 10/25/24 (a)		235		236
New Residential Mortgage Loan Trust
3.23%, 8/25/60 (a)		205		206
New Residential Mortgage Loan Trust,
3.75%, 5/28/52 — 8/25/55 (a)(b)		235		255
4.00%, 9/25/57 (a)(b)		451		498
NRPL Trust
4.25%, 7/25/67 (a)		554		572
OBX Trust
4.00%, 7/25/58 (a)(b)		278		283
Oceanview Mortgage Loan Trust
1.73%, 5/28/50 (a)		900		902
Pepper Residential Securities Trust,
1 Month USD LIBOR + 0.88%, 1.03%, 1/16/60 (a)(b)		240		239
1 Month USD LIBOR + 0.93%, 1.08%, 3/12/61 (a)(b)		595		593
1 Month USD LIBOR + 0.95%, 1.10%, 8/18/60 (a)(b)		306		305
1 Month USD LIBOR + 1.00%, 1.16%, 6/20/60 (a)(b)		327		326
Preston Ridge Partners LLC
1.00%, 9/25/25		1,200		1,200
PRPM LLC,
3.50%, 10/25/24 (a)(b)		693		695
4.50%, 1/25/24 (a)		498		502

	Face Amount (000)		Value (000)
Resimac, Series 19-2A 1 Month USD LIBOR + 0.95%, 1.11%, 2/10/51 (a)(b)	$	539	$	538
RESIMAC Bastille Trust,
1 Month USD LIBOR + 0.85%, 1.00%, 12/5/59 (a)(b)		199		198
1 Month USD LIBOR + 0.93%, 1.08%, 9/5/57 (a)(b)		382		382
RMF Buyout Issuance Trust,
1.71%, 6/25/30 (a)(b)		632		634
2.16%, 2/25/30 (a)(b)		1,724		1,728
Seasoned Credit Risk Transfer Trust
3.00%, 2/25/59		814		869
Sequoia Mortgage Trust
1 Month USD LIBOR + 0.62%, 0.78%, 8/20/34 (b)		168		163
Silver Hill Trust
3.10%, 11/25/49 (a)(b)		1,146		1,169
TVC Mortgage Trust
3.47%, 9/25/24 (a)		300		306
Vista Point Securitization Trust
1.76%, 3/25/65 (a)(b)		1,154		1,163
				22,935
Sovereign (1.3%)
Corp. Andina de Fomento,
1.63%, 9/23/25		1,750		1,756
2.38%, 5/12/23		1,170		1,215
Korea Development Bank (The)
3.00%, 3/19/22		410		424
Korea National Oil Corp.
0.88%, 10/5/25 (a)(c)		1,680		1,674
				5,069
Total Fixed Income Securities (Cost $350,070)				354,918
	Shares
Investment Company (3.0%)
iShares Short-Term Corporate Bond ETF (Cost $11,547)		210,000		11,531
Short-Term Investments (5.0%)
Investment Company (2.4%)
Morgan Stanley Institutional Liquidity Funds — Government Portfolio — Institutional Class (See Note G) (Cost $9,160)9,159,604				9,160
	Face Amount (000)
U.S. Treasury Securities (2.3%)
U.S. Treasury Bill 0.16%, 1/28/21 (d)	$	1,350		1,350
U.S. Treasury Notes
0.13%, 7/31/22		7,500		7,500
Total U.S. Treasury Securities (Cost $8,846)				8,850

The accompanying notes are an integral part of the financial statements.
13

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Short Duration Income Portfolio

	Face Amount (000)		Value (000)
Corporate Bond (0.3%)
Industrial (0.3%)
Marathon Petroleum Corp. 3.40%, 12/15/20 (Cost $1,278)	$	1,275	$	1,279
Total Short-Term Investments (Cost $19,284)				19,289
Total Investments (100.6%) (Cost $380,901) (e)(f)				385,738
Liabilities in Excess of Other Assets (–0.6%)				(2,271	)
Net Assets (100.0%)			$	383,467

(a)  144A security — Certain conditions for public sale may exist. Unless otherwise noted, these securities are deemed to be liquid.

(b)  Floating or variable rate securities: The rates disclosed are as of September 30, 2020. For securities based on a published reference rate and spread, the reference rate and spread are indicated in the description in the Portfolio of Investments. Certain variable rate securities may not be based on a published reference rate and spread but are determined by the issuer or agent and are based on current market conditions. These securities do not indicate a reference rate and spread in their description in the Portfolio of Investments.

(c)  When-issued security.

(d)  Rate shown is the yield to maturity at September 30, 2020.

(e)  Securities are available for collateral in connection with purchase of when-issued security and futures contracts.

(f)  At September 30, 2020, the aggregate cost for federal income tax purposes is approximately $380,798,000. The aggregate gross unrealized appreciation is approximately $5,800,000 and the aggregate gross unrealized depreciation is approximately $967,000, resulting in net unrealized appreciation of approximately $4,833,000.

@  Face Amount/Value is less than $500.

CMT  Constant Maturity Treasury Note Rate.

ETF  Exchange Traded Fund.

LIBOR  London Interbank Offered Rate.

MTN  Medium Term Note.

REMIC  Real Estate Mortgage Investment Conduit.

USD  United States Dollar.

Futures Contracts:

The Fund had the following futures contracts open at September 30, 2020:

	Number of Contracts		Expiration Date	Notional Amount (000)			Value (000)			Unrealized Appreciation (Depreciation) (000)
Long:
U.S. Treasury 2 yr. Note (United States)		505	Dec-20	$	101,000		$	111,585		$	50
Short:
U.S. Treasury 5 yr. Note (United States)		724	Dec-20		(72,400	)		(91,246	)		(153	)
										$	(103	)

Portfolio Composition

Classification	Percentage of Total Investments
Industrials		33.5	%
Finance		31.5
Asset-Backed Securities		13.1
Other*		11.0
Mortgages — Other		5.9
Short-Term Investments		5.0
Total Investments		100.0	%**

*  Industries and/or investment types representing less than 5% of total investments.

**  Does not include open long/short futures contracts with a value of approximately $202,831,000 and net unrealized depreciation of approximately $103,000.

The accompanying notes are an integral part of the financial statements.
14

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Short Duration Income Portfolio

Statement of Assets and Liabilities	September 30, 2020 (000)
Assets:
Investments in Securities of Unaffiliated Issuers, at Value (Cost $371,741)	$	376,578
Investment in Security of Affiliated Issuer, at Value (Cost $9,160)		9,160
Total Investments in Securities, at Value (Cost $380,901)		385,738
Receivable for Investments Sold		2,659
Receivable for Fund Shares Sold		2,192
Interest and Paydown Receivable		1,850
Receivable for Variation Margin on Futures Contracts		61
Due from Adviser		45
Receivable from Affiliate		—	@
Other Assets		77
Total Assets		392,622
Liabilities:
Payable for Investments Purchased		8,659
Payable for Fund Shares Redeemed		247
Payable for Professional Fees		72
Payable for Trustees' Fees and Expenses		41
Payable for Sub Transfer Agency Fees — Class I		25
Payable for Sub Transfer Agency Fees — Class A		14
Payable for Sub Transfer Agency Fees — Class L		—	@
Payable for Sub Transfer Agency Fees — Class C		—	@
Payable for Shareholder Services Fees — Class A		27
Payable for Distribution and Shareholder Services Fees — Class L		—	@
Payable for Distribution and Shareholder Services Fees — Class C		—	@
Payable for Administration Fees		23
Payable for Transfer Agency Fees — Class I		1
Payable for Transfer Agency Fees — Class A		1
Payable for Transfer Agency Fees — Class L		—	@
Payable for Transfer Agency Fees — Class C		1
Payable for Transfer Agency Fees — Class IS		1
Payable for Custodian Fees		4
Other Liabilities		39
Total Liabilities		9,155
Net Assets	$	383,467
Net Assets Consist of:
Paid-in-Capital	$	382,768
Total Distributable Earnings		699
Net Assets	$	383,467

The accompanying notes are an integral part of the financial statements.
15

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Short Duration Income Portfolio

Statement of Assets and Liabilities (cont'd)	September 30, 2020 (000)
CLASS I:
Net Assets	$	233,816
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		28,121,786
Net Asset Value, Offering and Redemption Price Per Share	$	8.31
CLASS A:
Net Assets	$	148,771
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		17,845,843
Net Asset Value, Redemption Price Per Share	$	8.34
Maximum Sales Load		2.00	%
Maximum Sales Charge	$	0.17
Maximum Offering Price Per Share	$	8.51
CLASS L:
Net Assets	$	829
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		99,764
Net Asset Value, Offering and Redemption Price Per Share	$	8.31
CLASS C:
Net Assets	$	37
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		4,492
Net Asset Value, Offering and Redemption Price Per Share	$	8.29
CLASS IS:
Net Assets	$	14
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		1,679
Net Asset Value, Offering and Redemption Price Per Share	$	8.32

@  Amount is less than $500.

The accompanying notes are an integral part of the financial statements.
16

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Short Duration Income Portfolio

Statement of Operations	Year Ended September 30, 2020 (000)
Investment Income:
Interest from Securities of Unaffiliated Issuers (Net of $—@ of Foreign Taxes Withheld)	$	6,363
Dividends from Security of Affiliated Issuer (Note G)		46
Dividends from Securities of Unaffiliated Issuers		10
Total Investment Income		6,419
Expenses:
Advisory Fees (Note B)		534
Shareholder Services Fees — Class A (Note D)		224
Distribution and Shareholder Services Fees — Class L (Note D)		4
Distribution and Shareholder Services Fees — Class C (Note D)		—	@
Sub Transfer Agency Fees — Class I		146
Sub Transfer Agency Fees — Class A		68
Sub Transfer Agency Fees — Class L		—	@
Sub Transfer Agency Fees — Class C		—	@
Administration Fees (Note C)		214
Professional Fees		174
Registration Fees		103
Shareholder Reporting Fees		57
Pricing Fees		35
Custodian Fees (Note F)		23
Transfer Agency Fees — Class I (Note E)		5
Transfer Agency Fees — Class A (Note E)		5
Transfer Agency Fees — Class L (Note E)		2
Transfer Agency Fees — Class C (Note E)		2
Transfer Agency Fees — Class IS (Note E)		2
Trustees' Fees and Expenses		10
Other Expenses		26
Total Expenses		1,634
Waiver of Advisory Fees (Note B)		(508	)
Reimbursement of Class Specific Expenses — Class I (Note B)		(62	)
Reimbursement of Class Specific Expenses — Class A (Note B)		(28	)
Reimbursement of Class Specific Expenses — Class L (Note B)		(2	)
Reimbursement of Class Specific Expenses — Class C (Note B)		(2	)
Reimbursement of Class Specific Expenses — Class IS (Note B)		(2	)
Rebate from Morgan Stanley Affiliate (Note G)		(16	)
Net Expenses		1,014
Net Investment Income		5,405
Realized Loss:
Investments Sold		(113	)
Futures Contracts		(1,743	)
Net Realized Loss		(1,856	)
Change in Unrealized Appreciation (Depreciation):
Investments		3,173
Foreign Currency Translation		—	@
Futures Contracts		133
Net Change in Unrealized Appreciation (Depreciation)		3,306
Net Realized Loss and Change in Unrealized Appreciation (Depreciation)		1,450
Net Increase in Net Assets Resulting from Operations	$	6,855

@  Amount is less than $500.

The accompanying notes are an integral part of the financial statements.
17

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Short Duration Income Portfolio

Statements of Changes in Net Assets	Year Ended September 30, 2020 (000)			Year Ended September 30, 2019 (000)
Increase (Decrease) in Net Assets:
Operations:
Net Investment Income	$	5,405		$	5,662
Net Realized Gain (Loss)		(1,856	)		750
Net Change in Unrealized Appreciation (Depreciation)		3,306			2,470
Net Increase in Net Assets Resulting from Operations		6,855			8,882
Dividends and Distributions to Shareholders:
Class I		(4,012	)		(3,777	)
Class A		(1,778	)		(1,635	)
Class L		(15	)		(13	)
Class C		(—	@)		(1	)
Class IS		(1	)		(—	@)
Total Dividends and Distributions to Shareholders		(5,806	)		(5,426	)
Capital Share Transactions:(1)
Class I:
Subscribed		159,179			140,638
Distributions Reinvested		3,802			3,751
Redeemed		(104,693	)		(90,693	)
Class A:
Subscribed		92,883			33,774
Distributions Reinvested		1,770			1,622
Redeemed		(29,414	)		(21,842	)
Class L:
Exchanged		44			656
Distributions Reinvested		15			13
Redeemed		(32	)		(270	)
Class C:
Distributions Reinvested		—	@		1
Redeemed		—			(16	)
Class IS:
Subscribed		35			5
Distributions Reinvested		1			—	@
Redeemed		(39	)		(—	@)
Net Increase in Net Assets Resulting from Capital Share Transactions		123,551			67,639
Total Increase in Net Assets		124,600			71,095
Net Assets:
Beginning of Period		258,867			187,772
End of Period	$	383,467		$	258,867

The accompanying notes are an integral part of the financial statements.
18

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Short Duration Income Portfolio

Statements of Changes in Net Assets (cont'd)	Year Ended September 30, 2020 (000)			Year Ended September 30, 2019 (000)
(1)   Capital Share Transactions:
Class I:
Shares Subscribed		19,301			17,226
Shares Issued on Distributions Reinvested		463			460
Shares Redeemed		(12,867	)		(11,081	)
Net Increase in Class I Shares Outstanding		6,897			6,605
Class A:
Shares Subscribed		11,183			4,121
Shares Issued on Distributions Reinvested		215			198
Shares Redeemed		(3,611	)		(2,670	)
Net Increase in Class A Shares Outstanding		7,787			1,649
Class L:
Shares Exchanged		5			81
Shares Issued on Distributions Reinvested		2			2
Shares Redeemed		(4	)		(34	)
Net Increase in Class L Shares Outstanding		3			49
Class C:
Shares Issued on Distributions Reinvested		—	@@		—	@@
Shares Redeemed		—			(2	)
Net Increase (Decrease) in Class C Shares Outstanding		—	@@		(2	)
Class IS:
Shares Subscribed		5			1
Shares Issued on Distributions Reinvested		—	@@		—	@@
Shares Redeemed		(5	)		(—	@@)
Net Increase (Decrease) in Class IS Shares Outstanding		(—	@@)		1

@  Amount is less than $500.

@@  Amount is less than 500 shares.

The accompanying notes are an integral part of the financial statements.
19

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Short Duration Income Portfolio

	Class I
	Year Ended September 30,
Selected Per Share Data and Ratios	2020			2019			2018			2017			2016(1)
Net Asset Value, Beginning of Period	$	8.24		$	8.13		$	8.15		$	8.12		$	7.71
Income (Loss) from Investment Operations:
Net Investment Income(2)		0.17			0.21			0.17			0.16			0.15
Net Realized and Unrealized Gain (Loss)		0.09			0.10			(0.03	)		0.02			0.41
Total from Investment Operations		0.26			0.31			0.14			0.18			0.56
Distributions from and/or in Excess of:
Net Investment Income		(0.19	)		(0.20	)		(0.16	)		(0.15	)		(0.15	)
Net Asset Value, End of Period	$	8.31		$	8.24		$	8.13		$	8.15		$	8.12
Total Return(3)		3.20	%		3.93	%(4)		1.79	%(5)		2.29	%(6)		7.43	%(7)
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	233,816		$	174,909		$	118,810		$	103,131		$	98,603
Ratio of Expenses Before Expense Limitation		0.53	%		0.49	%		0.50	%		0.53	%		0.65	%
Ratio of Expenses After Expense Limitation		0.29	%(8)		0.30	%(8)		0.28	%(8)		0.30	%(8)		0.36	%(8)(9)
Ratio of Net Investment Income		2.12	%(8)		2.55	%(8)		2.13	%(8)		1.92	%(8)		1.97	%(8)(9)
Ratio of Rebate from Morgan Stanley Affiliates		0.01	%		0.00	%(10)		0.00	%(10)		0.00	%(10)		0.00	%(10)
Portfolio Turnover Rate		74	%		64	%		40	%		43	%		66	%

(1)  Reflects prior period custodian out-of-pocket expenses that were reimbursed in September 2016. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class I shares. The Ratio of Expenses After Expense Limitation and the Ratio of Net Investment Income would be unchanged as the reimbursement of custodian fees was offset against expense waivers/reimbursements with no impact to net expenses or net investment income.

(2)  Per share amount is based on average shares outstanding.

(3)  Calculated based on the net asset value as of the last business day of the period.

(4)  Performance was positively impacted by approximately 0.13% due to the receipt of proceeds from the settlement of a class action suit involving the Fund's past holdings. This was a one-time settlement, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had this settlement not occurred, the total return for Class I shares would have been approximately 3.80%.

(5)  Performance was positively impacted by approximately 0.25% due to the receipt of proceeds from the settlement of class action suits involving the Fund's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class I shares would have been approximately 1.54%.

(6)  Performance was positively impacted by approximately 0.51% due to the receipt of proceeds from the settlement of a class action suit involving the Fund's past holdings. This was a one-time settlement, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had this settlement not occurred, the total return for Class I shares would have been approximately 1.78%.

(7)  Performance was positively impacted by approximately 5.97% due to the receipt of proceeds from the settlement of class action suits involving the Fund's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class I shares would have been approximately 1.46%.

(8)  The Ratio of Expenses After Expense Limitation and Ratio of Net Investment Income reflect the rebate of certain Fund expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates."

(9)  Effective January 11, 2016, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 0.30% for Class I shares. Prior to January 11, 2016, the maximum ratio was 0.53% for Class I shares.

(10)  Amount is less than 0.005%.

The accompanying notes are an integral part of the financial statements.
20

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Short Duration Income Portfolio

	Class A
	Year Ended September 30,
Selected Per Share Data and Ratios	2020			2019			2018			2017			2016(1)
Net Asset Value, Beginning of Period	$	8.26		$	8.15		$	8.17		$	8.13		$	7.72
Income (Loss) from Investment Operations:
Net Investment Income(2)		0.15			0.19			0.15			0.14			0.14
Net Realized and Unrealized Gain (Loss)		0.10			0.10			(0.03	)		0.03			0.40
Total from Investment Operations		0.25			0.29			0.12			0.17			0.54
Distributions from and/or in Excess of:
Net Investment Income		(0.17	)		(0.18	)		(0.14	)		(0.13	)		(0.13	)
Net Asset Value, End of Period	$	8.34		$	8.26		$	8.15		$	8.17		$	8.13
Total Return(3)		3.06	%		3.66	%(4)		1.51	%(5)		2.15	%(6)		7.15	%(7)
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	148,771		$	83,111		$	68,517		$	82,157		$	66,821
Ratio of Expenses Before Expense Limitation		0.77	%		0.76	%		0.80	%		0.80	%		0.80	%
Ratio of Expenses After Expense Limitation		0.54	%(8)		0.55	%(8)		0.55	%(8)		0.55	%(8)		0.52	%(8)(9)
Ratio of Net Investment Income		1.85	%(8)		2.30	%(8)		1.85	%(8)		1.66	%(8)		1.83	%(8)(9)
Ratio of Rebate from Morgan Stanley Affiliates		0.01	%		0.00	%(10)		0.00	%(10)		0.00	%(10)		0.00	%(10)
Portfolio Turnover Rate		74	%		64	%		40	%		43	%		66	%

(1)  Reflects prior period custodian out-of-pocket expenses that were reimbursed in September 2016. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class A shares. The Ratio of Expenses After Expense Limitation and the Ratio of Net Investment Income would be unchanged as the reimbursement of custodian fees was offset against expense waivers/reimbursements with no impact to net expenses or net investment income.

(2)  Per share amount is based on average shares outstanding.

(3)  Calculated based on the net asset value which does not reflect sales charges, if applicable, as of the last business day of the period.

(4)  Performance was positively impacted by approximately 0.13% due to the receipt of proceeds from the settlement of a class action suit involving the Fund's past holdings. This was a one-time settlement, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had this settlement not occurred, the total return for Class A shares would have been approximately 3.53%.

(5)  Performance was positively impacted by approximately 0.25% due to the receipt of proceeds from the settlement of class action suits involving the Fund's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class A shares would have been approximately 1.26%.

(6)  Performance was positively impacted by approximately 0.50% due to the receipt of proceeds from the settlement of a class action suit involving the Fund's past holdings. This was a one-time settlement, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had this settlement not occurred, the total return for Class A shares would have been approximately 1.65%.

(7)  Performance was positively impacted by approximately 5.94% due to the receipt of proceeds from the settlement of class action suits involving the Fund's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class A shares would have been approximately 1.21%.

(8)  The Ratio of Expenses After Expense Limitation and Ratio of Net Investment Income reflect the rebate of certain Fund expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates."

(9)  Effective January 11, 2016, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 0.55% for Class A shares. Prior to January 11, 2016, the maximum ratio was 0.88% for Class A shares.

(10)  Amount is less than 0.005%.

The accompanying notes are an integral part of the financial statements.
21

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Short Duration Income Portfolio

	Class L
	Year Ended September 30,
Selected Per Share Data and Ratios	2020			2019			2018			2017			2016(1)
Net Asset Value, Beginning of Period	$	8.24		$	8.12		$	8.15		$	8.11		$	7.70
Income (Loss) from Investment Operations:
Net Investment Income(2)		0.13			0.17			0.13			0.11			0.11
Net Realized and Unrealized Gain (Loss)		0.09			0.11			(0.04	)		0.04			0.41
Total from Investment Operations		0.22			0.28			0.09			0.15			0.52
Distributions from and/or in Excess of:
Net Investment Income		(0.15	)		(0.16	)		(0.12	)		(0.11	)		(0.11	)
Net Asset Value, End of Period	$	8.31		$	8.24		$	8.12		$	8.15		$	8.11
Total Return(3)		2.69	%		3.52	%(4)		1.14	%(5)		1.90	%(6)		6.79	%(7)
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	829		$	795		$	382		$	410		$	403
Ratio of Expenses Before Expense Limitation		1.26	%		1.25	%		1.52	%		1.70	%		1.83	%
Ratio of Expenses After Expense Limitation		0.79	%(8)		0.80	%(8)		0.80	%(8)		0.80	%(8)		0.92	%(8)(9)
Ratio of Net Investment Income		1.64	%(8)		2.07	%(8)		1.61	%(8)		1.41	%(8)		1.42	%(8)(9)
Ratio of Rebate from Morgan Stanley Affiliates		0.01	%		0.00	%(10)		0.00	%(10)		0.00	%(10)		0.00	%(10)
Portfolio Turnover Rate		74	%		64	%		40	%		43	%		66	%

(1)  Reflects prior period custodian out-of-pocket expenses that were reimbursed in September 2016. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class L shares. The Ratio of Expenses After Expense Limitation and the Ratio of Net Investment Income would be unchanged as the reimbursement of custodian fees was offset against expense waivers/reimbursements with no impact to net expenses or net investment income.

(2)  Per share amount is based on average shares outstanding.

(3)  Calculated based on the net asset value as of the last business day of the period.

(4)  Performance was positively impacted by approximately 0.13% due to the receipt of proceeds from the settlement of a class action suit involving the Fund's past holdings. This was a one-time settlement, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had this settlement not occurred, the total return for Class L shares would have been approximately 3.39%.

(5)  Performance was positively impacted by approximately 0.25% due to the receipt of proceeds from the settlement of class action suits involving the Fund's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class L shares would have been approximately 0.89%.

(6)  Performance was positively impacted by approximately 0.51% due to the receipt of proceeds from the settlement of a class action suit involving the Fund's past holdings. This was a one-time settlement, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had this settlement not occurred, the total return for Class L shares would have been approximately 1.39%.

(7)  Performance was positively impacted by approximately 5.92% due to the receipt of proceeds from the settlement of class action suits involving the Fund's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class L shares would have been approximately 0.87%.

(8)  The Ratio of Expenses After Expense Limitation and Ratio of Net Investment Income reflect the rebate of certain Fund expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates."

(9)  Effective January 11, 2016, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 0.80% for Class L shares. Prior to January 11, 2016, the maximum ratio was1.23% for Class L shares.

(10)  Amount is less than 0.005%.

The accompanying notes are an integral part of the financial statements.
22

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Short Duration Income Portfolio

	Class C
	Year Ended September 30,
Selected Per Share Data and Ratios	2020			2019			2018			2017			2016(1)
Net Asset Value, Beginning of Period	$	8.22		$	8.10		$	8.13		$	8.09		$	7.69
Income (Loss) from Investment Operations:
Net Investment Income(2)		0.09			0.13			0.09			0.07			0.07
Net Realized and Unrealized Gain (Loss)		0.09			0.11			(0.04	)		0.04			0.41
Total from Investment Operations		0.18			0.24			0.05			0.11			0.48
Distributions from and/or in Excess of:
Net Investment Income		(0.11	)		(0.12	)		(0.08	)		(0.07	)		(0.08	)
Net Asset Value, End of Period	$	8.29		$	8.22		$	8.10		$	8.13		$	8.09
Total Return(3)		2.16	%		3.01	%(4)		0.64	%(5)		1.34	%(6)		6.24	%(7)
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	37		$	36		$	52		$	52		$	95
Ratio of Expenses Before Expense Limitation		7.65	%		6.34	%		5.69	%		4.92	%		3.95	%
Ratio of Expenses After Expense Limitation		1.29	%(8)		1.30	%(8)		1.30	%(8)		1.30	%(8)		1.39	%(8)(9)
Ratio of Net Investment Income		1.14	%(8)		1.55	%(8)		1.11	%(8)		0.85	%(8)		0.93	%(8)(9)
Ratio of Rebate from Morgan Stanley Affiliates		0.01	%		0.00	%(10)		0.00	%(10)		0.00	%(10)		0.00	%(10)
Portfolio Turnover Rate		74	%		64	%		40	%		43	%		66	%

(1)  Reflects prior period custodian out-of-pocket expenses that were reimbursed in September 2016. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class C shares. The Ratio of Expenses After Expense Limitation and the Ratio of Net Investment Income would be unchanged as the reimbursement of custodian fees was offset against expense waivers/reimbursements with no impact to net expenses or net investment income.

(2)  Per share amount is based on average shares outstanding.

(3)  Calculated based on the net asset value which does not reflect sales charges, if applicable, as of the last business day of the period.

(4)  Performance was positively impacted by approximately 0.13% due to the receipt of proceeds from the settlement of a class action suit involving the Fund's past holdings. This was a one-time settlement, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had this settlement not occurred, the total return for Class C shares would have been approximately 2.88%.

(5)  Performance was positively impacted by approximately 0.25% due to the receipt of proceeds from the settlement of class action suits involving the Fund's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class C shares would have been approximately 0.39%.

(6)  Performance was positively impacted by approximately 0.50% due to the receipt of proceeds from the settlement of class action suits involving the Fund's past holdings. This was a one-time settlement, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had this settlement not occurred, the total return for Class C shares would have been approximately 0.84%.

(7)  Performance was positively impacted by approximately 5.77% due to the receipt of proceeds from the settlement of class action suits involving the Fund's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class C shares would have been approximately 0.47%.

(8)  The Ratio of Expenses After Expense Limitation and Ratio of Net Investment Income reflect the rebate of certain Fund expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates."

(9)  Effective January 11, 2016, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 1.30% for Class C shares. Prior to January 11, 2016, the maximum ratio was 1.63% for Class C shares.

(10)  Amount is less than 0.005%.

The accompanying notes are an integral part of the financial statements.
23

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Short Duration Income Portfolio

	Class IS
	Year Ended September 30,												Period from January 11, 2016(2) to
Selected Per Share Data and Ratios	2020			2019			2018			2017			September 30, 2016(1)
Net Asset Value, Beginning of Period	$	8.24		$	8.13		$	8.15		$	8.11		$	7.65
Income (Loss) from Investment Operations:
Net Investment Income(3)		0.18			0.21			0.18			0.16			0.17
Net Realized and Unrealized Gain (Loss)		0.09			0.11			(0.03	)		0.04			0.39
Total from Investment Operations		0.27			0.32			0.15			0.20			0.56
Distributions from and/or in Excess of:
Net Investment Income		(0.19	)		(0.21	)		(0.17	)		(0.16	)		(0.10	)
Net Asset Value, End of Period	$	8.32		$	8.24		$	8.13		$	8.15		$	8.11
Total Return(4)		3.37	%		3.98	%(5)		1.83	%(6)		2.46	%(7)		7.42	%(8)(11)
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	14		$	16		$	11		$	11		$	11
Ratio of Expenses Before Expense Limitation		12.15	%		17.44	%		18.54	%		16.24	%		17.12	%(12)
Ratio of Expenses After Expense Limitation		0.24	%(9)		0.24	%(9)		0.25	%(9)		0.25	%(9)		0.25	%(9)(12)
Ratio of Net Investment Income		2.21	%(9)		2.61	%(9)		2.16	%(9)		1.96	%(9)		2.20	%(9)(12)
Ratio of Rebate from Morgan Stanley Affiliates		0.01	%		0.00	%(10)		0.00	%(10)		0.00	%(10)		0.00	%(10)(12)
Portfolio Turnover Rate		74	%		64	%		40	%		43	%		66	%(11)

(1)  Reflects prior period custodian out-of-pocket expenses that were reimbursed in September 2016. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class IS shares. The Ratio of Expenses After Expense Limitation and the Ratio of Net Investment Income would be unchanged as the reimbursement of custodian fees was offset against expense waivers/reimbursements with no impact to net expenses or net investment income.

(2)  Commencement of Offering.

(3)  Per share amount is based on average shares outstanding.

(4)  Calculated based on the net asset value as of the last business day of the period.

(5)  Performance was positively impacted by approximately 0.13% due to the receipt of proceeds from the settlement of a class action suit involving the Fund's past holdings. This was a one-time settlement, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had this settlement not occurred, the total return for Class IS shares would have been approximately 3.85%.

(6)  Performance was positively impacted by approximately 0.25% due to the receipt of proceeds from the settlement of class action suits involving the Fund's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class IS shares would have been approximately 1.58%.

(7)  Performance was positively impacted by approximately 0.51% due to the receipt of proceeds from the settlement of a class action suit involving the Fund's past holdings. This was a one-time settlement, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had this settlement not occurred, the total return for Class IS shares would have been approximately 1.95%.

(8)  Performance was positively impacted by approximately 5.96% due to the receipt of proceeds from the settlement of class action suits involving the Fund's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class IS shares would have been approximately 1.46%.

(9)  The Ratio of Expenses After Expense Limitation and Ratio of Net Investment Income reflect the rebate of certain Fund expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates."

(10)  Amount is less than 0.005%.

(11)  Not annualized.

(12)  Annualized.

The accompanying notes are an integral part of the financial statements.
24

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements

Morgan Stanley Institutional Fund Trust ("Trust'') is registered under the Investment Company Act of 1940, as amended (the "Act''), as an open-end management investment company. The Trust is comprised of twelve separate, active funds (individually referred to as a "Fund," collectively as the "Funds"). The Trust applies investment company accounting and reporting guidance. All Funds are considered diversified for purposes of the Act.

The accompanying financial statements relate to the Short Duration Income Portfolio. The Fund seeks above-average total return over a market cycle of three to five years. The Fund offers five classes of shares — Class I, Class A, Class L, Class C and Class IS.

The Fund has suspended offering Class L and Class C shares to all investors. Class L and Class C shareholders of the Fund do not have the option of purchasing additional Class L and Class C shares, respectively. However, existing Class L and Class C shareholders may invest in additional Class L and Class C shares through reinvestment of dividends and distributions.

A. Significant Accounting Policies: The following significant accounting policies are in conformity with U.S. generally accepted accounting principles ("GAAP"). Such policies are consistently followed by the Trust in the preparation of its financial statements. GAAP may require management to make estimates and assumptions that affect the reported amounts and disclosures in the financial statements. Actual results may differ from those estimates.

In March 2017, the Financial Accounting Standards Board ("FASB") issued an Accounting Standard Update, ASU 2017-08, Receivables-Nonrefundable Fees and Other Costs (Subtopic 310-20), Premium Amortization on Purchased Callable Debt Securities ("ASU 2017-08") which amends the amortization period for certain purchased callable debt securities held at a premium, shortening such period to the earliest call date. ASU 2017-08 does not require any accounting change for debt securities held at a discount; the discount continues to be accreted to maturity. ASU 2017-08 is effective for fiscal years, and interim periods within those fiscal years, beginning after December 15, 2018. The adoption resulted in a change in accounting principle, since the Fund had historically amortized such premiums to maturity for U.S. GAAP. Accordingly, the Fund has adopted ASU 2017-08 to amend the premium amortization period for certain purchased callable debt securities with non-contingent call features to the

earliest call date. It is impracticable to evaluate the effect on individual prior periods, therefore the Fund applied the amendments on a modified retrospective basis by recognizing a cumulative effect adjustment that decreased the beginning of period cost of investments and increased the unrealized appreciation on investments of approximately $3,000.

This change in accounting policy has been made to comply with the newly issued accounting standard and had no impact on total accumulated earnings (loss) or the net asset value of the Fund. With respect to the Fund's results of operations, amortization of premium to first call date accelerates amortization with the intent of more closely aligning the recognition of income on such bonds with the economics of the instrument.

In March 2020, FASB issued an Accounting Standard Update, ASU 2020-04, Reference Rate Reform (Topic 848) — Facilitation of the Effects of Reference Rate Reform on Financial Reporting ("ASU 2020-04"), which provides optional, temporary relief with respect to the financial reporting of contracts subject to certain types of modifications due to the planned discontinuation of the London Interbank Offered Rate ("LIBOR") and other IBOR-based reference rates at the end of 2021. The temporary relief provided by ASU 2020-04 is effective for certain reference rate-related contract modifications that occur during the period from March 12, 2020 through December 31, 2022. Management is evaluating the impact of ASU 2020-04 on the Fund's investments, derivatives, debt and other contracts that will undergo reference rate-related modifications as a result of the reference rate reform.

1.  Security Valuation: (1) Certain portfolio securities may be valued by an outside pricing service/vendor approved by the Trust's Board of Trustees (the "Trustees"). The pricing service/vendor may employ a pricing model that takes into account, among other things, bids, yield spreads and/or other market data and specific security characteristics. Alternatively, if a valuation is not available from an outside pricing service/vendor, and the security trades on an exchange, the security may be valued at its latest reported sale price (or at the exchange official closing price if such exchange reports an official closing price), prior to the time when assets are valued. If there are no sales on a given day and if there is no official exchange closing price for that day, the security is valued at the mean between the last reported bid and asked prices if such bid and asked prices are available in the relevant exchanges. If only bid prices are available then the latest bid price may be used. If

25

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

Morgan Stanley Investment Management Inc. (the "Adviser"), a wholly-owned subsidiary of Morgan Stanley, determines that the price provided by the outside pricing service/vendor or exchange does not reflect the security's fair value or is unable to provide a price, prices from brokers or dealers may also be utilized. In these circumstances, the value of the security will be the mean of bid and asked prices obtained from brokers or dealers; (2) futures are valued at the settlement price on the exchange on which they trade or, if a settlement price is unavailable, at the last sale price on the exchange; (3) when market quotations are not readily available, including circumstances under which the Adviser determines that the closing price, last sale price or the mean between the last reported bid and asked prices are not reflective of a security's market value, portfolio securities are valued at their fair value as determined in good faith under procedures established by and under the general supervision of the Trustees. Occasionally, developments affecting the closing prices of securities and other assets may occur between the times at which valuations of such securities are determined (that is, close of the foreign market on which the securities trade) and the close of business of the New York Stock Exchange ("NYSE"). If developments occur during such periods that are expected to materially affect the value of such securities, such valuations may be adjusted to reflect the estimated fair value of such securities as of the close of the NYSE, as determined in good faith by the Trustees or by the Adviser using a pricing service and/or procedures approved by the Trustees; (4) quotations of foreign portfolio securities, other assets and liabilities and forward contracts stated in foreign currency are translated into U.S. dollar equivalents at the prevailing market rates prior to the close of the NYSE; and (5) investments in mutual funds, including the Morgan Stanley Institutional Liquidity Funds, are valued at the net asset value ("NAV") as of the close of each business day.

The Trustees have responsibility for determining in good faith the fair value of the investments, and the Trustees may appoint others, such as the Trust's Adviser or a valuation committee, to assist the Trustees in determining fair value and to make the actual calculations pursuant to the fair valuation methodologies previously approved by the Trustees. Under procedures approved by the Trustees, the Trust's Adviser has formed a Valuation Committee whose members are approved by the Trustees. The Valuation Committee provides

administration and oversight of the Trust's valuation policies and procedures, which are reviewed at least annually by the Trustees. These procedures allow the Trust to utilize independent pricing services, quotations from securities and financial instrument dealers and other market sources to determine fair value.

2.  Fair Value Measurement: FASB Accounting Standards Codification^TM ("ASC") 820, "Fair Value Measurement" ("ASC 820"), defines fair value as the value that the Fund would receive to sell an investment or pay to transfer a liability in a timely transaction with an independent buyer in the principal market, or in the absence of a principal market, the most advantageous market for the investment or liability. ASC 820 establishes a three-tier hierarchy to distinguish between (1) inputs that reflect the assumptions market participants would use in valuing an asset or liability developed based on market data obtained from sources independent of the reporting entity (observable inputs) and (2) inputs that reflect the reporting entity's own assumptions about the assumptions market participants would use in valuing an asset or liability developed based on the best information available in the circumstances (unobservable inputs) and to establish classification of fair value measurements for disclosure purposes. Various inputs are used in determining the value of the Fund's investments. The inputs are summarized in the three broad levels listed below:

•  Level 1 – unadjusted quoted prices in active markets for identical investments

•  Level 2 – other significant observable inputs (including quoted prices for similar investments, interest rates, prepayment speeds, credit risk, etc.)

•  Level 3 – significant unobservable inputs including the Fund's own assumptions in determining the fair value of investments. Factors considered in making this determination may include, but are not limited to, information obtained by contacting the issuer, analysts, or the appropriate stock exchange (for exchange-traded securities), analysis of the issuer's financial statements or other available documents and, if necessary, available information concerning other securities in similar circumstances.

26

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

The inputs or methodology used for valuing securities are not necessarily an indication of the risk associated with investing in those securities and the determination of the significance of a particular input to the fair value measurement in its entirety requires judgment and considers factors specific to each security.

The following is a summary of the inputs used to value the Fund's investments as of September 30, 2020:

Investment Type	Level 1 Unadjusted quoted prices (000)			Level 2 Other significant observable inputs (000)		Level 3 Significant unobservable inputs (000)		Total (000)
Assets:
Fixed Income Securities
Agency Adjustable Rate Mortgages	$	—		$	904	$	—	$	904
Agency Bond — Consumer Discretionary (U.S. Government Guaranteed)		—			297		—		297
Agency Fixed Rate Mortgages		—			1,275		—		1,275
Asset-Backed Securities		—			50,416		—		50,416
Collateralized Mortgage Obligations — Agency Collateral Series		—			1,023		—		1,023
Commercial Mortgage-Backed Securities		—			4,461		—		4,461
Corporate Bonds		—			268,538		—		268,538
Mortgages — Other		—			22,935		—		22,935
Sovereign		—			5,069		—		5,069
Total Fixed Income Securities		—			354,918		—		354,918
Investment Company		11,531			—		—		11,531
Short-Term Investments
Corporate Bond		—			1,279		—		1,279
Investment Company		9,160			—		—		9,160
U.S. Treasury Securities		—			8,850		—		8,850
Total Short-Term Investments		9,160			10,129		—		19,289
Futures Contracts		50			—		—		50
Total Assets		20,741			365,047		—		385,788
Liabilities:
Futures Contracts		(153	)		—		—		(153	)
Total	$	20,588		$	365,047	$	—	$	385,635

Transfers between investment levels may occur as the markets fluctuate and/or the availability of data used in an investment's valuation changes.

3.  Foreign Currency Translation and Foreign Investments: The books and records of the Fund are maintained in U.S. dollars. Foreign currency amounts are translated into U.S. dollars as follows:

–  investments, other assets and liabilities at the prevailing rate of exchange on the valuation date;

–  investment transactions and investment income at the prevailing rates of exchange on the dates of such transactions.

Although the net assets of the Fund are presented at the foreign exchange rates and market values at the close of the period, the Fund does not isolate that portion of the results of operations arising as a result of changes in the foreign exchange rates from the fluctuations arising from changes in the market prices of securities held at period end. Similarly, the Fund does not isolate the effect of changes in foreign exchange rates from the fluctuations arising from changes in the market prices of securities sold during the period. Accordingly, realized and unrealized foreign currency gains (losses) on investments in securities are included in the reported net realized and unrealized gains (losses) on investment transactions and balances. However, pursuant to U.S. federal income tax regulations, gains and losses from certain foreign currency transactions and the foreign currency portion of gains and losses realized on sales and maturities of foreign denominated debt securities are treated as ordinary income for U.S. federal income tax purposes.

Net realized gains (losses) on foreign currency transactions represent net foreign exchange gains (losses) from currency gains (losses) realized between the trade and settlement dates on securities transactions, and the difference between the amount of investment income and foreign withholding taxes recorded on the Fund's books and the U.S. dollar equivalent amounts actually received or paid. The change in unrealized currency gains (losses) on foreign currency transactions for the period is reflected in the Statement of Operations.

Foreign security and currency transactions may involve certain considerations and risks not typically associated with those of U.S. dollar denominated transactions as a result of, among other factors, fluctuations of exchange rates in relation to the U.S. dollar, the possibility of lower levels of governmental supervision and regulation

27

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

of foreign securities markets and the possibility of political or economic instability.

Governmental approval for foreign investments may be required in advance of making an investment under certain circumstances in some countries, and the extent of foreign investments in domestic companies may be subject to limitation in other countries. Foreign ownership limitations also may be imposed by the charters of individual companies to prevent, among other concerns, violations of foreign investment limitations. As a result, an additional class of shares (identified as "Foreign" in the Portfolio of Investments) may be created and offered for investment. The "local" and "foreign shares" market values may differ. In the absence of trading of the foreign shares in such markets, the Fund values the foreign shares at the closing exchange price of the local shares.

4.  Derivatives: The Fund may, but is not required to, use derivative instruments for a variety of purposes, including hedging, risk management, portfolio management or to earn income. Derivatives are financial instruments whose value is based, in part, on the value of an underlying asset, interest rate, index or financial instrument. Prevailing interest rates and volatility levels, among other things, also affect the value of derivative instruments. A derivative instrument often has risks similar to its underlying asset and may have additional risks, including imperfect correlation between the value of the derivative and the underlying asset, risks of default by the counterparty to certain transactions, magnification of losses incurred due to changes in the market value of the securities, instruments, indices or interest rates to which the derivative instrument relates, risks that the transactions may not be liquid and risks arising from margin requirements. The use of derivatives involves risks that are different from, and possibly greater than, the risks associated with other portfolio investments. Derivatives may involve the use of highly specialized instruments that require investment techniques and risk analyses different from those associated with other portfolio investments. All of the Fund's holdings, including derivative instruments, are marked-to-market each day with the change in value reflected in unrealized appreciation (depreciation). Upon disposition, a realized gain or loss is recognized.

Certain derivative transactions may give rise to a form of leverage. Leverage magnifies the potential for gain and the risk of loss. Leverage associated with derivative

transactions may cause the Fund to liquidate portfolio positions when it may not be advantageous to do so to satisfy its obligations or to meet earmarking or segregation requirements, pursuant to applicable Securities and Exchange Commission ("SEC") rules and regulations, or may cause the Fund to be more volatile than if the Fund had not been leveraged. Although the Adviser seeks to use derivatives to further the Fund's investment objectives, there is no assurance that the use of derivatives will achieve this result.

Following is a description of the derivative instruments and techniques that the Fund used during the period and their associated risks:

Futures: A futures contract is a standardized, exchange-traded agreement to buy or sell a specific quantity of an underlying asset, reference rate or index at a specific price at a specific future time. The value of a futures contract tends to increase and decrease in tandem with the value of the underlying instrument. Depending on the terms of the particular contract, futures contracts are settled through either physical delivery of the underlying instrument on the settlement date or by payment of a cash settlement amount on the settlement date. During the period the futures contract is open, payments are received from or made to the broker based upon changes in the value of the contract (the variation margin). A decision as to whether, when and how to use futures contracts involves the exercise of skill and judgment and even a well-conceived futures transaction may be unsuccessful because of market behavior or unexpected events. In addition to the derivatives risks discussed above, the prices of futures contracts can be highly volatile, using futures contracts can lower total return and the potential loss from futures contracts can exceed the Fund's initial investment in such contracts. No assurance can be given that a liquid market will exist for any particular futures contract at any particular time. There is also the risk of loss by the Fund of margin deposits in the event of bankruptcy of a broker with which the Fund has open positions in the futures contract.

FASB ASC 815, "Derivatives and Hedging" ("ASC 815"), is intended to improve financial reporting about derivative instruments by requiring enhanced disclosures to enable investors to better understand how and why the Fund uses derivative instruments, how these derivative instruments are accounted for and their

28

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

effects on the Fund's financial position and results of operations.

The following tables set forth the fair value of the Fund's derivative contracts by primary risk exposure as of September 30, 2020:

	Asset Derivatives Statement of Assets and Liabilities Location	Primary Risk Exposure	Value (000)
Futures Contract	Variation Margin on Futures Contract	Interest Rate Risk	$	50	(a)
	Liability Derivatives Statement of Assets and Liabilities Location	Primary Risk Exposure	Value (000)
Futures Contract	Variation Margin on Futures Contract	Interest Rate Risk	$	(153	)(a)

(a) This amount represents the cumulative appreciation (depreciation) as reported in the Portfolio of Investments. The Statement of Assets and Liabilities only reflects the current day's net variation margin.

The following tables set forth by primary risk exposure the Fund's realized gains (losses) and change in unrealized appreciation (depreciation) by type of derivative contract for the year ended September 30, 2020 in accordance with ASC 815:

Realized Gain (Loss)
Primary Risk Exposure	Derivative Type	Value (000)
Interest Rate Risk	Futures Contracts	$	(1,743	)
Change in Unrealized Appreciation (Depreciation)
Primary Risk Exposure	Derivative Type	Value (000)
Interest Rate Risk	Futures Contracts	$	133

For the year ended September 30, 2020, the approximate average monthly amount outstanding for each derivative type is as follows:

Futures Contracts:
Average monthly notional value	$	157,935,000

5.  When-Issued/Delayed Delivery Securities: The Fund purchases and sells when-issued and delayed delivery securities. Securities purchased on a when-issued or delayed delivery basis are purchased for delivery beyond the normal settlement date at a stated price and yield, and no income accrues to the Fund on such securities prior to delivery date. Payment and delivery for when-issued and delayed delivery securities can take place a month or more after the date of the transaction. When the Fund enters into a purchase transaction on a when-issued or delayed delivery basis, securities are available for collateral in an amount at least equal in value to the Fund's commitments to purchase such securities. Purchasing securities on a when-issued or delayed delivery basis may involve a risk

that the market price at the time of delivery may be lower than the agreed upon purchase price, in which case there could be an unrealized loss at the time of delivery. Purchasing investments on a when-issued or delayed delivery basis may be considered a form of leverage which may increase the impact that gains (losses) may have on the Fund.

6.  Indemnifications: The Trust enters into contracts that contain a variety of indemnifications. The Trust's maximum exposure under these arrangements is unknown. However, the Trust has not had prior claims or losses pursuant to these contracts and expects the risk of loss to be remote.

7.  Dividends and Distributions to Shareholders: Dividends and distributions to shareholders are recorded on the ex-dividend date. Dividends from net investment income, if any, are declared and paid monthly. Net realized capital gains, if any, are distributed at least annually.

8.  Security Transactions, Income and Expenses: Security transactions are accounted for on the trade date (date the order to buy or sell is executed). Realized gains and losses on the sale of investment securities are determined on the specific identified cost method. Dividend income and other distributions are recorded on the ex-dividend date (except for certain foreign dividends which may be recorded as soon as the Fund is informed of such dividends) net of applicable withholding taxes. Interest income is recognized on the accrual basis except where collection is in doubt. Discounts are accreted and premiums are amortized over the life of the respective securities. Most expenses of the Trust can be directly attributed to a particular Fund. Expenses which cannot be directly attributed are apportioned among the Funds based upon relative net assets or other appropriate methods. Income, expenses (other than class specific expenses — distribution and shareholder services, transfer agency and sub transfer agency fees) and realized and unrealized gains or losses are allocated to each class of shares based upon their relative net assets.

B. Advisory Fees: The Adviser, a wholly-owned subsidiary of Morgan Stanley, provides the Fund with advisory services under the terms of an Investment Advisory Agreement, paid quarterly, at an annual rate of 0.20% of the average daily net assets of the Fund.

29

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

The Adviser has agreed to reduce its advisory fee and/or reimburse the Fund so that total annual Fund operating expenses, excluding certain investment related expenses, taxes, interest and other extraordinary expenses (including litigation), will not exceed 0.30% for Class I shares, 0.55% for Class A shares, 0.80% for Class L shares, 1.30% for Class C shares and 0.25% for Class IS shares. The fee waivers and/or expense reimbursements will continue for at least one year or until such time as the Trustees act to discontinue all or a portion of such waivers and/or reimbursements when they deem such action is appropriate. For the year ended September 30, 2020, approximately $508,000 of advisory fees were waived and approximately $96,000 of other expenses were reimbursed by the Adviser pursuant to this arrangement.

C. Administration Fees: The Adviser also serves as Administrator to the Trust and provides administrative services pursuant to an Administration Agreement for an annual fee, accrued daily and paid monthly, of 0.08% of the Fund's average daily net assets. Under a Sub-Administration Agreement between the Administrator and State Street Bank and Trust Company ("State Street"), State Street provides certain administrative services to the Trust. For such services, the Administrator pays State Street a portion of the fee the Administrator receives from the Fund.

D. Distribution and Shareholder Services Fees: Morgan Stanley Distribution, Inc. ("MSDI" or the "Distributor"), a wholly-owned subsidiary of the Adviser, and an indirect subsidiary of Morgan Stanley, serves as the Trust's Distributor of Fund shares pursuant to a Distribution Agreement. The Trust has adopted a Shareholder Services Plan with respect to Class A shares pursuant to Rule 12b-1 under the Act. Under the Shareholder Services Plan, the Fund pays the Distributor a shareholder services fee, accrued daily and paid monthly, at an annual rate of 0.25% of the Fund's average daily net assets attributable to Class A shares.

The Trust has adopted a Distribution and Shareholder Services Plan with respect to Class L shares pursuant to Rule 12b-1 under the Act. Under the Distribution and Shareholder Services Plan, the Fund pays the Distributor a distribution fee, accrued daily and paid monthly, at an annual rate of 0.25% and a shareholder services fee, accrued daily and paid monthly, at an annual rate of 0.25% of the Fund's average daily net assets attributable to Class L shares.

The Trust has adopted a Distribution and Shareholder Services Plan with respect to Class C shares pursuant to Rule 12b-1 under the Act. Under the Distribution and Shareholder Services

Plan, the Fund pays the Distributor a distribution fee, accrued daily and paid monthly, at an annual rate of 0.75% and a shareholder services fee, accrued daily and paid monthly, at an annual rate of 0.25% of the Fund's average daily net assets attributable to Class C shares.

The distribution and shareholder services fees are used to support the expenses associated with servicing and maintaining accounts. The Distributor may compensate other parties for providing shareholder support services to investors who purchase Class A, Class L and Class C shares.

E. Dividend Disbursing and Transfer/Co-Transfer Agent: The Trust's dividend disbursing and transfer agent is DST Asset Manager Solutions, Inc. ("DST"). Pursuant to a Transfer Agency Agreement, the Trust pays DST a fee based on the number of classes, accounts and transactions relating to the Funds of the Trust.

Morgan Stanley Services Company Inc. serves as Co-Transfer Agent and provides certain transfer agency services to the Fund with respect to certain direct transactions with the Fund.

F. Custodian Fees: State Street (the "Custodian") also serves as Custodian for the Trust in accordance with a Custodian Agreement. The Custodian holds cash, securities and other assets of the Trust as required by the Act. Custody fees are payable monthly based on assets held in custody, investment purchases and sales activity and account maintenance fees, plus reimbursement for certain out-of-pocket expenses.

G. Security Transactions and Transactions with Affiliates: For the year ended September 30, 2020, purchases and sales of investment securities for the Fund, other than long-term U.S. Government securities and short-term investments were approximately $303,448,000 and $175,180,000, respectively. For the year ended September 30, 2020, purchases and sales of long-term U.S. Government securities were approximately $5,286,000 and $12,926,000, respectively.

The Fund invests in the Institutional Class of the Morgan Stanley Institutional Liquidity Funds — Government Portfolio (the "Liquidity Funds"), an open-end management investment company managed by the Adviser. Advisory fees paid by the Fund are reduced by an amount equal to its pro-rata share of the advisory and administration fees paid by the Fund due to its investment in the Liquidity Funds. For the year ended September 30, 2020, advisory fees paid were reduced by approximately $16,000 relating to the Fund's investment in the Liquidity Funds.

30

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

A summary of the Fund's transactions in shares of affiliated investments during the year ended September 30, 2020 is as follows:

Affiliated Investment Company	Value September 30, 2019 (000)		Purchases at Cost (000)		Proceeds from Sales (000)		Dividend Income (000)
Liquidity Funds	$	10,033	$	215,844	$	216,717	$	46

Affiliated Investment Company (cont'd)	Realized Gain (Loss) (000)		Change in Unrealized Appreciation (Depreciation) (000)		Value September 30, 2020 (000)
Liquidity Funds	$	—	$	—	$	9,160

The Fund is permitted to purchase and sell securities ("cross-trade") from and to other Morgan Stanley funds as well as other funds and client accounts for which the Adviser or an affiliate of the Adviser serves as investment adviser, pursuant to procedures approved by the Trustees in compliance with Rule 17a-7 under the Act (the "Rule"). Each cross-trade is executed at the current market price in compliance with provisions of the Rule. For the year ended September 30, 2020, the Fund did not engage in any cross-trade transactions.

The Fund has an unfunded Deferred Compensation Plan (the "Compensation Plan"), which allows each independent Trustee to defer payment of all, or a portion, of the fees he or she receives for serving on the Board of Trustees. Each eligible Trustee generally may elect to have the deferred amounts credited with a return equal to the total return on one or more of the Morgan Stanley funds that are offered as investment options under the Compensation Plan. Appreciation/depreciation and distributions received from these investments are recorded with an offsetting increase/decrease in the deferred compensation obligation and do not affect the NAV of the Fund.

H. Federal Income Taxes: It is the Fund's intention to continue to qualify as a regulated investment company and distribute all of its taxable and tax-exempt income. Accordingly, no provision for federal income taxes is required in the financial statements.

The Fund may be subject to taxes imposed by countries in which it invests. Such taxes are generally based on income and/or capital gains earned or repatriated. Taxes are accrued based on net investment income, net realized gains and net unrealized appreciation as such income and/or gains are earned. Taxes may also be based on transactions in foreign currency and are accrued based on the value of investments denominated in such currency.

FASB ASC 740-10, "Income Taxes — Overall", sets forth a minimum threshold for financial statement recognition of the benefit of a tax position taken or expected to be taken in a tax return. Management has concluded there are no significant uncertain tax positions that would require recognition in the financial statements. If applicable, the Fund recognizes interest accrued related to unrecognized tax benefits in "Interest Expense" and penalties in "Other Expenses" in the Statement of Operations. The Fund files tax returns with the U.S. Internal Revenue Service, New York and various states. Generally, each of the tax years in the four-year period ended September 30, 2020 remains subject to examination by taxing authorities.

The tax character of distributions paid may differ from the character of distributions shown for GAAP purposes due to short-term capital gains being treated as ordinary income for tax purposes. The tax character of distributions paid during fiscal years 2020 and 2019 was as follows:

2020 Distributions Paid From: Ordinary Income (000)		2019 Distributions Paid From: Ordinary Income (000)
$	5,806	$	5,426

The amount and character of income and gains to be distributed are determined in accordance with income tax regulations which may differ from GAAP. These book/tax differences are either considered temporary or permanent in nature.

Temporary differences are attributable to differing book and tax treatments for the timing of the recognition of gains (losses) on certain investment transactions and the timing of the deductibility of certain expenses.

Permanent differences, due to tax adjustments on callable bonds, resulted in the following reclassifications among the components of net assets at September 30, 2020:

Total Distributable Earnings (000)		Paid-in- Capital (000)
$	34	$	(34	)

At September 30, 2020, the components of distributable earnings for the Fund on a tax basis were as follows:

Undistributed Ordinary Income (000)		Undistributed Long-Term Capital Gain (000)
$	694	$	—

31

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

At September 30, 2020, the Fund had available for federal income tax purposes unused short-term and long-term capital losses of approximately $1,728,000 and $3,046,000, respectively, that do not have an expiration date.

To the extent that capital loss carryforwards are used to offset any future capital gains realized, no capital gains tax liability will be incurred by the Fund for gains realized and not distributed. To the extent that capital gains are offset, such gains will not be distributed to the shareholders.

I. Credit Facility: The Trust and other Morgan Stanley funds participated in a $300,000,000 committed, unsecured revolving line of credit facility (the "Facility") with State Street. This Facility is to be used for temporary emergency purposes or funding of shareholder redemption requests. The interest rate on borrowings is based on the federal funds rate or 1 month LIBOR rate plus a spread. The Facility also has a commitment fee of 0.25% per annum based on the unused portion of the Facility. During the year ended September 30, 2020, the Fund did not have any borrowings under the Facility.

J. Other: At September 30, 2020, the Fund had record owners of 10% or greater. Investment activities of these shareholders could have a material impact on the Fund. The aggregate percentage of such owners was 67.2%.

K. Market Risk: Certain impacts to public health conditions particular to the coronavirus (COVID-19) outbreak could impact the operations and financial performance of certain of the Fund's investments. The extent of the impact to the financial performance of the Fund's investments will depend on future developments, including (i) the duration and spread of the outbreak, (ii) the restrictions and advisories, (iii) the effects on the financial markets, and (iv) the effects on the economy overall, all of which are highly uncertain and cannot be predicted. If the financial performance of the Fund's investments is impacted because of these factors for an extended period, the Fund's investment results may be adversely affected.

L. LIBOR Risk: The Fund's investments, payment obligations and financing terms may be based on floating rates, such as London Interbank Offer Rate ("LIBOR"), Euro Interbank Offered Rate and other similar types of reference rates (each, a "Reference Rate"). These Reference Rates are generally intended to represent the rate at which contributing banks may obtain short-term borrowings from each other within certain financial markets. On July 27, 2017, the Chief Executive of

the UK Financial Conduct Authority ("FCA"), which regulates LIBOR, announced that the FCA will no longer persuade nor require banks to submit rates for the calculation of LIBOR and certain other Reference Rates after 2021. Such announcement indicates that the continuation of LIBOR and other Reference Rates on the current basis cannot and will not be guaranteed after the end of 2021. This announcement and any additional regulatory or market changes may have an adverse impact on the Fund or its investments.

In advance of 2022, regulators and market participants are currently engaged in identifying successor Reference Rates ("Alternative Reference Rates"). Additionally, prior to the end of 2021, it is expected that market participants will focus on the transition mechanisms by which the Reference Rates in existing contracts or instruments may be amended, whether through marketwide protocols, fallback contractual provisions, bespoke negotiations or amendments or otherwise. Nonetheless, the termination of certain Reference Rates presents risks to the Fund. At this time, it is not possible to completely identify or predict the effect of any such changes, any establishment of Alternative Reference Rates or any other reforms to Reference Rates that may be enacted in the UK or elsewhere. The elimination of a Reference Rate or any other changes or reforms to the determination or supervision of Reference Rates could have an adverse impact on the market for or value of any securities or payments linked to those Reference Rates and other financial obligations held by the Fund or on its overall financial condition or results of operations.

32

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Report of Independent Registered Public Accounting Firm

To the Shareholders and Board of Trustees of
Morgan Stanley Institutional Fund Trust —
Short Duration Income Portfolio

Opinion on the Financial Statements

We have audited the accompanying statement of assets and liabilities of Short Duration Income Portfolio (the "Fund") (one of the funds constituting Morgan Stanley Institutional Fund Trust (the "Trust")), including the portfolio of investments, as of September 30, 2020, and the related statement of operations for the year then ended, the statements of changes in net assets for each of the two years in the period then ended, the financial highlights for each of the five years in the period then ended and the related notes (collectively referred to as the "financial statements"). In our opinion, the financial statements present fairly, in all material respects, the financial position of the Fund (one of the funds constituting Morgan Stanley Institutional Fund Trust) at September 30, 2020, the results of its operations for the year then ended, the changes in its net assets for each of the two years in the period then ended and its financial highlights for each of the five years in the period then ended, in conformity with U.S. generally accepted accounting principles.

Basis for Opinion

These financial statements are the responsibility of the Trust's management. Our responsibility is to express an opinion on the Fund's financial statements based on our audits. We are a public accounting firm registered with the Public Company Accounting Oversight Board (United States) ("PCAOB") and are required to be independent with respect to the Trust in accordance with the U.S. federal securities law and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB.

We conducted our audits in accordance with the standards of the PCAOB. Those standards require that we plan and perform the audit to obtain reasonable assurance about whether the financial statements are free of material misstatement, whether due to error or fraud. The Trust is not required to have, nor were we engaged to perform, an audit of the Trust's internal control over financial reporting. As part of our audits we are required to obtain an understanding of internal control over financial reporting but not for the purpose of expressing an opinion on the effectiveness of the Trust's internal control over financial reporting. Accordingly, we express no such opinion.

Our audits included performing procedures to assess the risks of material misstatement of the financial statements, whether due to error or fraud, and performing procedures that respond to those risks. Such procedures included examining, on a test basis, evidence regarding the amounts and disclosures in the financial statements. Our procedures included confirmation of securities owned as of September 30, 2020 by correspondence with the custodian and brokers or by other appropriate auditing procedures where replies from brokers were not received. Our audits also included evaluating the accounting principles used and significant estimates made by management, as well as evaluating the overall presentation of the financial statements. We believe that our audits provide a reasonable basis for our opinion.

We have served as the auditor of one or more Morgan Stanley investment companies since 2000.
Boston, Massachusetts
November 24, 2020

33

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Advisory Agreement Approval (unaudited)

Nature, Extent and Quality of Services

The Board reviewed and considered the nature and extent of the investment advisory services provided by the Adviser under the advisory agreement, including portfolio management, investment research and equity and fixed income securities trading. The Board also reviewed and considered the nature and extent of the non-advisory, administrative services provided by the Administrator under the administration agreement, including accounting, operations, clerical, bookkeeping, compliance, business management and planning, legal services and the provision of supplies, office space and utilities at the Adviser's expense. The Board also considered the Adviser's investment in personnel and infrastructure that benefits the Fund. (The Adviser and Administrator together are referred to as the "Adviser" and the advisory and administration agreements together are referred to as the "Management Agreement.") The Board also considered that the Adviser serves a variety of other investment advisory clients and has experience overseeing service providers. The Board also compared the nature of the services provided by the Adviser with similar services provided by non-affiliated advisers as prepared by Broadridge Financial Solutions, Inc. ("Broadridge").

The Board reviewed and considered the qualifications of the portfolio managers, the senior administrative managers and other key personnel of the Adviser who provide the advisory and administrative services to the Fund. The Board determined that the Adviser's portfolio managers and key personnel are well qualified by education and/or training and experience to perform the services in an efficient and professional manner. The Board concluded that the nature and extent of the advisory and administrative services provided were necessary and appropriate for the conduct of the business and investment activities of the Fund and supported its decision to approve the Management Agreement.

Performance, Fees and Expenses of the Fund

The Board reviewed the performance, fees and expenses of the Fund compared to its peers, as prepared by Broadridge, and to appropriate benchmarks where applicable. The Board discussed with the Adviser the performance goals and the actual results achieved in managing the Fund. When considering a fund's performance, the Board and the Adviser place emphasis on trends and longer-term returns (focusing on one-year, three-year and five-year performance, as of December 31, 2019, or since inception, as applicable). When a fund underperforms its benchmark and/or its peer group average, the Board and the Adviser discuss the causes of such underperformance and, where necessary, they discuss specific changes to investment strategy or investment personnel. The Board noted that the Fund's performance was better than its peer group average for the three- and five-year periods but below its peer group average for the one-year period. The Board discussed with the Adviser the level of the advisory and administration fees (together, the "management fee") for this Fund relative to comparable funds and/or other accounts advised by the Adviser and/or compared to its peers as prepared by Broadridge. In addition to the management fee, the Board also reviewed the Fund's total expense ratio. The Board noted that the Fund's management fee and total expense ratio were lower than its peer group averages. After discussion, the Board concluded that the Fund's performance, management fee and total expense ratio were competitive with its peer group averages.

Economies of Scale

The Board considered the size and growth prospects of the Fund and how that relates to the Fund's total expense ratio and particularly the Fund's management fee rate, which does not include breakpoints. In conjunction with its review of the Adviser's profitability, the Board discussed with the Adviser how a change in assets can affect the efficiency or effectiveness of managing the Fund and whether the management fee level is appropriate relative to current and projected asset levels and/or whether the management fee structure reflects economies of scale as asset levels change. The Board has determined that its review of the actual and/or potential economies of scale of the Fund supports its decision to approve the Management Agreement.

Profitability of the Adviser and Affiliates

The Board considered information concerning the costs incurred and profits realized by the Adviser and its affiliates during the last year from their relationship with the Fund and during the last two years from their relationship with the Morgan Stanley Fund Complex and reviewed with the Adviser the cost allocation methodology used to determine the profitability of the Adviser and affiliates. The Board has determined that its review of the analysis of the Adviser's expenses and profitability supports its decision to approve the Management Agreement.

34

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Advisory Agreement Approval (unaudited) (cont'd)

Other Benefits of the Relationship

The Board considered other direct and indirect benefits to the Adviser and/or its affiliates derived from their relationship with the Fund and other funds advised by the Adviser. These benefits may include, among other things, fees for trading, distribution and/or shareholder servicing and for transaction processing and reporting platforms used by securities lending agents, and research received by the Adviser generated from commission dollars spent on funds' portfolio trading. The Board reviewed with the Adviser these arrangements and the reasonableness of the Adviser's costs relative to the services performed. The Board has determined that its review of the other benefits received by the Adviser or its affiliates supports its decision to approve the Management Agreement.

Resources of the Adviser and Historical Relationship Between the Fund and the Adviser

The Board considered whether the Adviser is financially sound and has the resources necessary to perform its obligations under the Management Agreement. The Board also reviewed and considered the historical relationship between the Fund and the Adviser, including the organizational structure of the Adviser, the policies and procedures formulated and adopted by the Adviser for managing the Fund's operations and the Board's confidence in the competence and integrity of the senior managers and key personnel of the Adviser. The Board concluded that the Adviser has the financial resources necessary to fulfill its obligations under the Management Agreement and that it is beneficial for the Fund to continue its relationship with the Adviser.

Other Factors and Current Trends

The Board considered the controls and procedures adopted and implemented by the Adviser and monitored by the Fund's Chief Compliance Officer and concluded that the conduct of business by the Adviser indicates a good faith effort on its part to adhere to high ethical standards in the conduct of the Fund's business.

As part of the Board's review, the Board received information from management on the impact of COVID-19 on the firm generally and the Adviser and the Fund in particular including, among other information, the pandemic's current and expected impact on the Fund's performance and operations.

General Conclusion

After considering and weighing all of the above factors, with various written materials and verbal information presented by the Adviser, the Board concluded that it would be in the best interest of the Fund and its shareholders to approve renewal of the Management Agreement for another year. In reaching this conclusion the Board did not give particular weight to any single piece of information or factor referenced above. The Board considered these factors and information over the course of the year and in numerous meetings, some of which were in executive session with only the independent Board members and their counsel present. It is possible that individual Board members may have weighed these factors, and the information presented, differently in reaching their individual decisions to approve the Management Agreement.

35

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Liquidity Risk Management Program (unaudited)

In compliance with Rule 22e-4 under the Investment Company Act of 1940, as amended (the "Liquidity Rule"), the Fund has adopted and implemented a liquidity risk management program (the "Program"), which is reasonably designed to assess and manage the risk that the Fund could not meet requests to redeem shares issued by the Fund without significant dilution of remaining investors' interests in the Fund (i.e., liquidity risk). The Fund's Board of Trustees (the "Board") previously approved the designation of the Liquidity Risk Subcommittee (the "LRS") as Program administrator. The LRS is comprised of representatives from various divisions within Morgan Stanley Investment Management.

At a meeting held on April 22-23, 2020, the Board reviewed a written report prepared by the LRS that addressed the Program's operation and assessed its adequacy, and effectiveness of implementation for the period from December 1, 2018, through December 31, 2019, as required under the Liquidity Rule. The report concluded that the Program operated effectively and was adequately and effectively implemented in all material aspects, and that the relevant controls and safeguards were appropriately designed to enable the LRS to administer the Program in compliance with the Liquidity Rule.

In accordance with the Program, the LRS assessed each Fund's liquidity risk no less frequently than annually taking into consideration certain factors, as applicable, such as (i) investment strategy and liquidity of portfolio investments, (ii) short-term and long-term cash flow projections and (iii) holdings of cash and cash equivalents and borrowing arrangements and other funding sources. Certain factors are considered under both normal and reasonably foreseeable stressed conditions.

Each Fund portfolio investment is classified into one of four liquidity categories, which classification is assessed at least monthly by the LRS. The classification is based on a determination of the number of days it is reasonably expected to take to convert the investment into cash, or sell or dispose of the investment, in current market conditions without significantly changing the market value of the investment. Liquidity classification determinations take into account various market, trading and investment-specific considerations, as well as market depth, and in some cases utilize third-party vendor data.

The Liquidity Rule limits a fund's investments in illiquid investments to 15% of its net assets and requires funds that do not primarily hold assets that are highly liquid investments to determine and maintain a minimum percentage of the fund's net assets to be invested in highly liquid investments (highly liquid investment minimum or "HLIM"). The LRS believes that the Program includes provisions reasonably designed to review, monitor and comply with the 15% limit on illiquid investments and for determining, periodically reviewing and complying with the HLIM requirement, as applicable.

There can be no assurance that the Program will achieve its objectives under all circumstances in the future. Please refer to the Fund's prospectus for more information regarding the Fund's exposure to liquidity risk and other risks to which it may be subject.

36

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Privacy Notice (unaudited)  April 2019

FACTS	WHAT DOES MSIM DO WITH YOUR PERSONAL INFORMATION?
Why?	Financial companies choose how they share your personal information. Federal law gives consumers the right to limit some but not all sharing. Federal law also requires us to tell you how we collect, share, and protect your personal information. Please read this notice carefully to understand what we do.
What?	The types of personal information we collect and share depend on the product or service you have with us. This information can include: n Social Security number and income n investment experience and risk tolerance n checking account number and wire transfer instructions
How?	All financial companies need to share customers' personal information to run their everyday business. In the section below, we list the reasons financial companies can share their customers' personal information; the reasons MSIM chooses to share; and whether you can limit this sharing.

Reasons we can share your personal information	Does MSIM share?	Can you limit this sharing?
For our everyday business purposes — such as to process your transactions, maintain your account(s), respond to court orders and legal investigations, or report to credit bureaus	Yes	No
For our marketing purposes — to offer our products and services to you	Yes	No
For joint marketing with other financial companies	No	We don't share
For our affiliates' everyday business purposes — information about your transactions and experiences	Yes	No
For our affiliates' everyday business purposes — information about your creditworthiness	No	We don't share
For our affiliates to market to you	No	We don't share
For non-affiliates to market to you	No	We don't share

Questions?Call toll-free (844) 312-6327 or email: imprivacyinquiries@morganstanley.com

37

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Privacy Notice (unaudited) (cont'd)  April 2019

Who we are

Who is providing this notice? Morgan Stanley Investment Management, Inc. and its affiliated registered investment advisers, registered broker-dealers, and registered and unregistered funds ("MSIM")

What we do

How does MSIM protect my personal information?	To protect your personal information from unauthorized access and use, we use security measures that comply with federal law. These measures include computer safeguards and secured files and buildings. We have policies governing the proper handling of customer information by personnel and requiring third parties that provide support to adhere to appropriate security standards with respect to such information.
How does MSIM collect my personal information?	We collect your personal information, for example, when you n open an account or make deposits or withdrawals from your account n buy securities from us or make a wire transfer n give us your contact information We also collect your personal information from others, such as credit bureaus, affiliates, or other companies.
Why can't I limit all sharing?	Federal law gives you the right to limit only n sharing for affiliates' everyday business purposes — information about your creditworthiness n affiliates from using your information to market to you n sharing for non-affiliates to market to you State laws and individual companies may give you additional rights to limit sharing. See below for more on your rights under state law.

Definitions

Affiliates	Companies related by common ownership or control. They can be financial and non-financial companies. n Our affiliates include companies with a Morgan Stanley name and financial companies such as Morgan Stanley Smith Barney LLC and Morgan Stanley & Co.
Non-affiliates	Companies not related by common ownership or control. They can be financial and non-financial companies. n MSIM does not share with non-affiliates so they can market to you.
Joint marketing	A formal agreement between non-affiliated financial companies that together market financial products or services to you. n MSIM doesn't jointly market

Other Important Information

Vermont: Except as permitted by law, we will not share personal information we collect about Vermont residents with Non-affiliates unless you provide us with your written consent to share such information.

California: Except as permitted by law, we will not share personal information we collect about California residents with Non-affiliates and we will limit sharing such personal information with our Affiliates to comply with California privacy laws that apply to us.

38

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited)

Independent Trustees:

Name, Address and Birth Year of Independent Trustee	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years and Other Relevant Professional Experience	Number of Funds in Fund Complex Overseen by Independent Trustee**		Other Directorships Held by Independent Trustee***
Frank L. Bowman c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1944	Trustee	Since August 2006	President, Strategic Decisions, LLC (consulting) (since February 2009); Director or Trustee of various Morgan Stanley Funds (since August 2006); Chairperson of the Compliance and Insurance Committee (since October 2015); formerly, Chairperson of the Insurance Sub-Committee of the Compliance and Insurance Committee (2007-2015); served as President and Chief Executive Officer of the Nuclear Energy Institute (policy organization) (February 2005-November 2008); retired as Admiral, U.S. Navy after serving over 38 years on active duty including 8 years as Director of the Naval Nuclear Propulsion Program in the Department of the Navy and the U.S. Department of Energy (1996-2004); served as Chief of Naval Personnel (July 1994-September 1996) and on the Joint Staff as Director of Political Military Affairs (June 1992- July 1994); knighted as Honorary Knight Commander of the Most Excellent Order of the British Empire; awarded the Officier de l'Orde National du Mérite by the French Government; elected to the National Academy of Engineering (2009).		86	Director of Naval and Nuclear Technologies LLP; Director Emeritus of the Armed Services YMCA; Member of the National Security Advisory Council of the Center for U.S. Global Engagement and a member of the CNA Military Advisory Board; Trustee of Fairhaven United Methodist Church; Member of the Board of Advisors of the Dolphin Scholarship Foundation; Director of other various non-profit organizations; Formerly, Director of BP p.l.c. (November 2010-May 2019).
Kathleen A. Dennis c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1953	Trustee	Since August 2006	President, Cedarwood Associates (mutual fund and investment management consulting) (since July 2006); Chairperson of the Liquidity and Alternatives Sub-Committee of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 2006); formerly, Senior Managing Director of Victory Capital Management (1993-2006).		86	Director of various non-profit organizations.
Nancy C. Everett c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1955	Trustee	Since January 2015	Chief Executive Officer, Virginia Commonwealth University Investment Company (since November 2015); Owner, OBIR, LLC (institutional investment management consulting) (since June 2014); formerly, Managing Director, BlackRock, Inc. (February 2011-December 2013); and Chief Executive Officer, General Motors Asset Management (a/k/a Promark Global Advisors, Inc.) (June 2005-May 2010).		87	Formerly, Member of Virginia Commonwealth University School of Business Foundation (2005-2016); Member of Virginia Commonwealth University Board of Visitors (2013-2015); Member of Committee on Directors for Emerging Markets Growth Fund, Inc. (2007-2010); Chairperson of Performance Equity Management, LLC (2006-2010); and Chairperson, GMAM Absolute Return Strategies Fund, LLC (2006-2010).

39

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Address and Birth Year of Independent Trustee	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years and Other Relevant Professional Experience	Number of Funds in Fund Complex Overseen by Independent Trustee**		Other Directorships Held by Independent Trustee***
Jakki L. Haussler c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1957	Trustee	Since January 2015	Chairman, Opus Capital Group (since January 1996); formerly, Chief Executive Officer, Opus Capital Group (1996-2019); Director, Capvest Venture Fund, LP (May 2000-December 2011); Partner, Adena Ventures, LP (July 1999-December 2010); Director, The Victory Funds (February 2005-July 2008).		87	Director of Service Corporation International and Member, Audit Committee and Investment Committee; Director of Cincinnati Bell Inc. and Member, Audit Committee and Governance and Nominating Committee; Director of Northern Kentucky University Foundation and Member, Investment Committee; Member of Chase College of Law Transactional Law Practice Center Board of Advisors; Director of Chase College of Law Board of Visitors; formerly, Member, University of Cincinnati Foundation Investment Committee; Member, Miami University Board of Visitors (2008-2011); Trustee of Victory Funds (2005-2008) and Chairman, Investment Committee (2007-2008); Member, Service Provider Committee (2005-2008) and Director of Best Transport (2006-2019).
Dr. Manuel H. Johnson c/o Johnson Smick International, Inc. 220 I Street, NE — Suite 200 Washington, D.C. 20002 Birth Year 1949	Trustee	Since July 1991	Senior Partner, Johnson Smick International, Inc. (consulting firm); Chairperson of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since July 1991); Co-Chairman and a founder of the Group of Seven Council (G7C) (international economic commission); formerly, Chairperson of the Audit Committee (July 1991-September 2006), Vice Chairman of the Board of Governors of the Federal Reserve System and Assistant Secretary of the U.S. Treasury.		86	Director of NVR, Inc. (home construction).
Joseph J. Kearns c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1942	Trustee	Since August 1994	Senior Adviser, Kearns & Associates LLC (investment consulting); Chairperson of the Audit Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 1994); Director, Rubicorn Investments (since February 2019); formerly, Deputy Chairperson of the Audit Committee (July 2003-September 2006) and Chairperson of the Audit Committee of various Morgan Stanley Funds (since August 1994); CFO of the J. Paul Getty Trust (1982-1999).		87	Prior to August 10, 2016, Director of Electro Rent Corporation (equipment leasing); Prior to December 31, 2013, Director of The Ford Family Foundation.

40

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Address and Birth Year of Independent Trustee	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years and Other Relevant Professional Experience	Number of Funds in Fund Complex Overseen by Independent Trustee**		Other Directorships Held by Independent Trustee***
Michael F. Klein c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1958	Trustee	Since August 2006	Managing Director, Aetos Alternatives Management, LP (since March 2000); Co-President, Aetos Alternatives Management, LP (since January 2004) and Co-Chief Executive Officer of Aetos Alternatives Management, LP (since August 2013); Chairperson of the Fixed Income Sub-Committee of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 2006); formerly, Managing Director, Morgan Stanley & Co. Inc. and Morgan Stanley Dean Witter Investment Management and President, various Morgan Stanley Funds (June 1998-March 2000); Principal, Morgan Stanley & Co. Inc. and Morgan Stanley Dean Witter Investment Management (August 1997-December 1999).		86	Director of certain investment funds managed or sponsored by Aetos Alternatives Management, LP; Director of Sanitized AG and Sanitized Marketing AG (specialty chemicals).
Patricia Maleski c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1960	Trustee	Since January 2017	Managing Director, JPMorgan Asset Management (2004-2016); Oversight and Control Head of Fiduciary and Conflicts of Interest Program (2015-2016); Chief Control Officer-Global Asset Management (2013-2015); President, JPMorgan Funds (2010-2013); Chief Administrative Officer (2004-2013); various other positions including Treasurer and Board Liaison (since 2001).		87	None.
W. Allen Reed c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1947	Chair of the Board and Trustee	Chair of the Boards since August 2020 and Trustee since August 2006	Chair of the Boards of various Morgan Stanley Funds (since August 2020); Chairperson of the Governance Committee; Chairperson of the Equity Sub-Committee of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 2006); formerly, Vice Chair of the Boards of various Morgan Stanley Funds (January 2020-August 2020); President and Chief Executive Officer of General Motors Asset Management; Chairman and Chief Executive Officer of the GM Trust Bank and Corporate Vice President of General Motors Corporation (August 1994-December 2005).		86	Formerly, Director of Legg Mason, Inc. (2006-2019); and Director of the Auburn University Foundation (2010-2015).

*  This is the earliest date the Trustee began serving the Morgan Stanley Funds. Each Trustee serves an indefinite term, until his or her successor is elected.

**  The Fund Complex includes (as of December 31, 2019) all open-end and closed-end funds (including all of their portfolios) advised by Morgan Stanley Investment Management Inc. (the "Adviser") and any funds that have an adviser that is an affiliated person of the Adviser (including, but not limited to, Morgan Stanley AIP GP LP).

***  This includes any directorships at public companies and registered investment companies held by the Trustee at any time during the past five years.

41

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited) (cont'd)

Executive Officers:

Name, Address and Birth Year of Executive Officer	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years
John H. Gernon 522 Fifth Avenue New York, NY 10036 Birth Year 1963	President and Principal Executive Officer	Since September 2013	President and Principal Executive Officer of the Equity and Fixed Income Funds and the Morgan Stanley AIP Funds (since September 2013) and the Liquidity Funds and various money market funds (since May 2014) in the Fund Complex; Managing Director of the Adviser; Head of Public Markets Product Development (since 2006).
Timothy J. Knierim 522 Fifth Avenue New York, NY 10036 Birth Year 1959	Chief Compliance Officer	Since December 2016	Managing Director of the Adviser and various entities affiliated with the Adviser; Chief Compliance Officer of various Morgan Stanley Funds and the Adviser (since December 2016) and Chief Compliance Officer of Morgan Stanley AIP GP LP (since 2014). Formerly, Managing Director and Deputy Chief Compliance Officer of the Adviser (2014-2016); and formerly, Chief Compliance Officer of Prudential Investment Management, Inc. (2007-2014).
Francis J. Smith 522 Fifth Avenue New York, NY 10036 Birth Year 1965	Treasurer and Principal Financial Officer	Treasurer since July 2003 and Principal Financial Officer since September 2002	Managing Director of the Adviser and various entities affiliated with the Adviser; Treasurer (since July 2003) and Principal Financial Officer of various Morgan Stanley Funds (since September 2002).
Mary E. Mullin 522 Fifth Avenue New York, NY 10036 Birth Year 1967	Secretary	Since June 1999	Managing Director of the Adviser; Secretary of various Morgan Stanley Funds (since June 1999).
Michael J. Key 522 Fifth Avenue New York, NY 10036 Birth Year 1979	Vice President	Since June 2017	Vice President of the Equity and Fixed Income Funds, Liquidity Funds, various money market funds and the Morgan Stanley AIP Funds in the Fund Complex (since June 2017); Executive Director of the Adviser; Head of Product Development for Equity and Fixed Income Funds (since August 2013).

*  This is the earliest date the officer began serving the Morgan Stanley Funds. Each officer serves a one-year term, until his or her successor is elected and qualifies.

42

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Adviser and Administrator

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

Distributor

Morgan Stanley Distribution, Inc.
522 Fifth Avenue
New York, New York 10036

Dividend Disbursing and Transfer Agent

DST Asset Manager Solutions, Inc.
2000 Crown Colony Drive
Quincy, Massachusetts 02169

Co-Transfer Agent

Morgan Stanley Services Company, Inc.
522 Fifth Avenue
New York, New York 10036

Custodian

State Street Bank and Trust Company
One Lincoln Street
Boston, Massachusetts 02111

Legal Counsel

Dechert LLP
1095 Avenue of the Americas
New York, New York 10036

Counsel to the Independent Trustees

Perkins Coie LLP
1155 Avenue of the Americas,
22nd Floor
New York, New York 10036

Independent Registered Public Accounting Firm

Ernst & Young LLP
200 Clarendon Street
Boston, Massachusetts 02116

Reporting to Shareholders

Each Morgan Stanley fund provides a complete schedule of portfolio holdings in its Semi-Annual and the Annual Reports within 60 days of the end of the fund's second and fourth fiscal quarters. The Semi-Annual and Annual Reports are filed electronically with the Securities and Exchange Commission ("SEC") on Form N-CSRS and Form N-CSR, respectively. Morgan Stanley also delivers the Semi-Annual and Annual Reports to fund shareholders and makes these reports available on its public website, www.morganstanley.com/im/shareholderreports. Each Morgan Stanley non-money market fund also files a complete schedule of portfolio holdings with the SEC for the fund's first and third fiscal quarters as an attachment to Form N-PORT. Morgan Stanley does not deliver the reports for the first and third fiscal quarters to shareholders, nor are the reports posted to the Morgan Stanley public website. However, the holdings for each money market fund are posted to the Morgan Stanley public website. You may obtain the Form N-PORT filings (as well as the Form N-CSR and N-CSRS filings) by accessing the SEC's website, www.sec.gov. You can also request copies of these materials, upon payment of a duplicating fee, by electronic request at the SEC's email address (publicinfo@sec.gov).

Proxy Voting Policies and Procedures and Proxy Voting Record

You may obtain a copy of the Trust's Proxy Voting Policy and Procedures and information regarding how the Trust voted proxies relating to portfolio securities during the most recent twelve-month period ended June 30, without charge, upon request, by calling toll free 1 (800) 548-7786 or by visiting our website at www.morganstanley.com/im/shareholderreports. This information is also available on the SEC's website at www.sec.gov.

This report is authorized for distribution only when preceded or accompanied by a prospectus or summary prospectus of the applicable Fund of Morgan Stanley Institutional Fund Trust, which describes in detail the Fund's investment policies, risks, fees and expenses. Please read the prospectus carefully before you invest or send money. For additional information, including information regarding the investments comprising the Fund, please visit our website at www.morganstanley.com/im/shareholderreports or call toll free 1 (800) 548-7786.

43

Printed in U.S.A.
This Report has been prepared for shareholders and may be distributed to others only if preceded or accompanied by a current prospectus.

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

© 2020 Morgan Stanley. Morgan Stanley Distribution, Inc.

IFTLDANN
3298830 EXP 11.30.21

INVESTMENT MANAGEMENT

Morgan Stanley Institutional Fund Trust

Strategic Income Portfolio

Annual Report

September 30, 2020

Beginning on January 1, 2021, as permitted by regulations adopted by the Securities and Exchange Commission ("SEC"), paper copies of the Fund's Annual and Semi-Annual Reports to Shareholders ("Shareholder Reports") will no longer be sent by mail, unless you specifically request paper copies of the Shareholder Reports from the Fund or from your financial intermediary, such as a broker-dealer or a bank. Instead, the Shareholder Reports will be made available on the Fund's website, https://www.morganstanley.com/im/shareholderreports and you will be notified by mail each time a Shareholder Report is posted and provided with a website link to access the Shareholder Report. If you already elected to receive Shareholder Reports electronically, you will not be affected by this change and you need not take any action. You may elect to receive Shareholder Reports and other communications from the Fund electronically anytime by contacting your financial intermediary or, if you are a direct investor, please follow the instructions on the envelope.

Beginning on January 1, 2019, you may elect to receive all future Shareholder Reports in paper free of charge. If you invest through a financial intermediary, you can contact your financial intermediary to request that you continue to receive paper copies of your Shareholder Reports. If you invest directly with the Fund, please follow the instructions on the envelope to let the Fund know you wish to continue receiving paper copies of your Shareholder Reports. Your election to receive Shareholder Reports in paper will apply to all funds held in your account if you invest through your financial intermediary or all funds held with the fund complex if you invest directly with a fund.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Table of Contents

Shareholders' Letter	2
Expense Example	3
Investment Overview	4
Portfolio of Investments	8
Statement of Assets and Liabilities	14
Statement of Operations	16
Statements of Changes in Net Assets	17
Financial Highlights	18
Notes to Financial Statements	22
Report of Independent Registered Public Accounting Firm	33
Investment Advisory Agreement Approval	34
Liquidity Risk Management Program	36
Privacy Notice	37
Trustee and Officer Information	39

This report is authorized for distribution only when preceded or accompanied by a prospectus or summary prospectus of the applicable Fund of the Morgan Stanley Institutional Fund Trust. To receive a prospectus and/or statement of additional information ("SAI"), which contains more complete information such as investment objectives, charges, expenses, policies for voting proxies, risk considerations and describes in detail each of the Fund's investment policies to the prospective investor, please call toll free 1 (800) 548-7786. Please read the prospectuses carefully before you invest or send money.

Additionally, you can access information about the Fund, including performance, characteristics and investment team commentary, through Morgan Stanley Investment Management's website: www.morganstanley.com/im/shareholderreports.

Market forecasts provided in this report may not necessarily come to pass. There is no guarantee that any sectors mentioned will continue to perform as discussed herein or that securities in such sectors will be held by the Fund in the future. There is no assurance that a fund will achieve its investment objective. Funds are subject to market risk, which is the possibility that market values of securities owned by the Fund will decline and, therefore, the value of the Fund's shares may be less than what you paid for them. Accordingly, you can lose money investing in this Fund. Please see the prospectus for more complete information on investment risks.

1

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Shareholders' Letter (unaudited)

Dear Shareholders,

We are pleased to provide this Annual Report, in which you will learn how your investment in Strategic Income Portfolio (the "Fund") performed during the latest twelve-month period.

Morgan Stanley Investment Management is a client-centric, investor-led organization. Our global presence, intellectual capital, and breadth of products and services enable us to partner with investors to meet the evolving challenges of today's financial markets. We aim to deliver superior investment service and to empower our clients to make the informed decisions that help them reach their investment goals.

As always, we thank you for selecting Morgan Stanley Investment Management, and look forward to working with you in the months and years ahead.

Sincerely,

John H. Gernon
President and Principal Executive Officer

October 2020

2

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Expense Example (unaudited)

Strategic Income Portfolio

As a shareholder of the Fund, you may incur two types of costs: (1) transactional costs, including sales charge (loads) on purchase payments; and (2) ongoing costs, which may include advisory fees, administration fees, distribution and shareholder services fees; and other Fund expenses. This example is intended to help you understand your ongoing costs (in dollars) of investing in the Fund and to compare these costs with the ongoing costs of investing in other mutual funds.

This example is based on an investment of $1,000 invested at the beginning of the six-month period ended September 30, 2020 and held for the entire six-month period.

Actual Expenses

The table below provides information about actual account values and actual expenses. You may use the information in this table, together with the amount you invested, to estimate the expenses that you paid over the period. Simply divide your account value by $1,000 (for example, an $8,600 account value divided by $1,000 = 8.6), then multiply the result by the number in the table under the heading entitled "Actual Expenses Paid During Period" to estimate the expenses you paid on your account during this period.

Hypothetical Example for Comparison Purposes

The table below provides information about hypothetical account values and hypothetical expenses based on the Fund's actual expense ratio and an assumed rate of return of 5% per year before expenses, which is not the Fund's actual return. The hypothetical account values and expenses may not be used to estimate the actual ending account balance or expenses you paid for the period. You may use this information to compare the ongoing costs of investing in the Fund and other funds. To do so, compare this 5% hypothetical example with the 5% hypothetical examples that appear in the shareholder reports of the other funds.

Please note that the expenses shown in the table are meant to highlight your ongoing costs only and do not reflect any transactional costs, such as sales charges (loads, if applicable). Therefore, the information for each class in the table is useful in comparing ongoing costs only, and will not help you determine the relative total costs of owning different funds. In addition, if these transactional costs were included, your costs would have been higher.

	Beginning Account Value 4/1/20		Actual Ending Account Value 9/30/20		Hypothetical Ending Account Value		Actual Expenses Paid During Period*		Hypothetical Expenses Paid During Period*		Net Expense Ratio During Period**
Strategic Income Portfolio Class I	$	1,000.00	$	1,134.10	$	1,022.05	$	3.15	$	2.98		0.59	%
Strategic Income Portfolio Class A		1,000.00		1,132.10		1,020.25		5.06		4.80		0.95
Strategic Income Portfolio Class C		1,000.00		1,127.40		1,016.50		9.04		8.57		1.70
Strategic Income Portfolio Class IS		1,000.00		1,132.90		1,022.15		3.04		2.88		0.57

*  Expenses are calculated using each Fund Class' annualized net expense ratio (as disclosed), multiplied by the average account value over the period and multiplied by 183/366 (to reflect the most recent one-half year period).

**  Annualized.

3

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Overview (unaudited)

Strategic Income Portfolio

The Fund seeks to maximize current income consistent with the preservation of capital.

Performance

For the fiscal year ended September 30, 2020, the Fund's Class I shares had a total return based on net asset value and reinvestment of distributions per share of 0.98%, net of fees. The Fund's Class I shares underperformed against the Fund's benchmark, the Bloomberg Barclays U.S. Aggregate Index, which returned 6.98%. Effective October 1, 2019, the Fund's primary benchmark changed to Bloomberg Barclays U.S. Aggregate Index because the Adviser believes the Bloomberg Barclays U.S. Aggregate Index is a more appropriate benchmark for the Fund's new investment objective and principal investment strategies also effective as of that date.ⁱ

Factors Affecting Performance

•  The positive total return was driven by macro decisions, notably the long duration position in the U.S. Over the past year, the Fund has held a positive duration between 2.2 and 3.1 years, which helped in February and March 2020 when the 10-year U.S. Treasury yield fell 120 basis points (bps). Since then, Treasury rates have remained relatively range-bound between 60 and 80 bps.

•  We expect rates to stay low, especially in the front end of the yield curve, for quite some time. In August 2020, the Federal Reserve (Fed) made the unprecedented, but widely expected, decision to revise its inflation strategy to achieve 2% inflation over time by allowing for intentional overshoots of the 2% target — called "flexible average inflation targeting." This revised framework implies that the Fed will not raise interest rates against a tight labor market without significant evidence of inflation.

•  The largest detractors from performance were the allocation to securitized credit, as well as the high yield and investment grade corporate bond exposure.

•  The allocation to securitized credit is composed of non-agency residential mortgage-backed securities (RMBS), asset-backed securities (ABS) and

commercial mortgage-backed securities (CMBS), with a bias to own housing credit. While this allocation has been the Fund's best performer over the past couple of months, the losses from the first quarter of 2020, when the pandemic led to a significant widening in risk assets, have not been fully recouped. The housing market has been resilient during the pandemic. As of September 30, 2020, the mortgage delinquency rate is at roughly 17%, well below the rate we saw in the 2008 financial crisis.ⁱⁱ

•  We have slowly reduced securitized credit risk, as spreads have recovered significantly but conditions have not substantially improved.

•  The allocation to high yield and investment grade corporate bonds shows a similar story. Although spreads have tightened significantly following the significant widening in the first quarter of 2020, the allocation has still not recouped the losses.

Management Strategies

•  Global growth is expected to contract in 2020 as COVID-19 has resulted in deep recessions across economies globally. The pace of the economic recovery appears to be slowing, as the support from pent-up demand fades and economies have to deal with renewed lockdowns as infection rates start to increase once again. While economic data in general continues to be better than expected, it seems unlikely that the current pace of upside surprises can be sustained. Many of the geopolitical risks that have troubled investors in the past — U.S.-China tensions, deadlock over renewed U.S. fiscal stimulus measures, Brexit, tensions between Russia and Europe — persist.

•  Corporate credit spreads have largely recovered to pre-pandemic levels as a result of the Fed's purchases of high yield and investment grade corporate exchange-traded funds. However, this good news is increasingly factored into prices, with credit spreads at, or below, their long-term averages in spite of the still challenging economic outlook, therefore offering investors yield advantage but limited capital gain potential. We remain long

ⁱ  Effective October 1, 2019, the Fund's investment objective changed to: "The Fund seeks to maximize current income consistent with the preservation of capital." In addition, effective as of the same date, the Fund's investment process, which currently incorporates information about ESG issues via an integrated approach within the portfolio management team's fundamental

investment analysis framework, transitioned to an investment process that utilizes ESG factors as fundamental drivers of credit risk and, in turn, a bond's return. Please refer to the Fund's prospectus dated January 28, 2020 for additional information.

ⁱⁱ  Source: Morgan Stanley Research

4

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Overview (unaudited) (cont'd)

Strategic Income Portfolio

credit risk, as our base case reflects the consensus view that COVID-19 is transitory and monetary policy will remain credit risk friendly, likely driving spreads tighter in the medium term. The strong market rally experienced over recent months makes positioning sensitive to valuations and technicals of supply and demand. Within high yield corporate debt, we expect to see a meaningful increase in overall defaults in the coming year due to a significantly weaker economy stemming from the outbreak, as well as stress in the energy sector. However, with a significant reduction in default activity over the last two months and a far quicker recovery from the COVID-19 shock than initially anticipated, we expect default rates to be a more muted 6% to 8%, as opposed to the 10% to 12% initially forecasted. While we remain cautiously optimistic that developments could lead to even tighter spreads by year-end or in 2021, we expect some near-term volatility as we approach the November election.

•  In the securitized assets sector, we remain cautiously optimistic as U.S. economic conditions remain weak, with jobless claims exceeding 60 million since March 2020 and COVID-19 infection rates continue to surge throughout the U.S. and Europe.ⁱⁱⁱ While positive developments on potential vaccines and treatments continue to be made, with several vaccines undergoing large-scale third-stage trials, realistically, any vaccine-related recovery likely remains a 2021 potential event.

•  U.S. non-agency mortgage-backed securities (MBS) valuations are mixed; newly originated, or 2.0 non-agency MBS, look expensive at current valuations, but attractive opportunities exist in legacy non-agency RMBS, non-performing loans and other non-traditional RMBS. We expect the U.S. housing market to remain stable and non-agency RMBS to continue to perform relatively well from a credit perspective in the fourth quarter of 2020.

•  U.S. ABS such as auto loans, credit cards and consumer loans have performed reasonably well during the pandemic. In fact, some securities, such as prime auto loans, have fully recovered to January 2020 levels. We have taken profits on those positions. The bonds' fundamentals look strong, but risks are higher, and we believe spreads should reflect that.

•  CMBS backed by hotels, retail shopping centers and aircraft ABS continue to lag behind sectors less impacted by the pandemic. Our largest allocation within CMBS is to multi-family housing and apartments. Single-family rentals are nearly back to pre-pandemic levels, and there is continued demand from people moving out of cities to the suburbs.

•  We remain cautiously constructive on emerging markets debt in the near term on the back of loose monetary policy in the developed world, recently boosted by the Fed's new strategy of average inflation targeting. We believe lower real yields in the U.S. and the resulting weaker dollar should be supportive of emerging markets fixed income, particularly in the high yield segment and currencies. Positive headlines on new vaccines and treatments for COVID-19 could also lift sentiment further. However, several macro risks persist such as heightened U.S.-China tensions (trade and technology issues/geopolitics), which are inflamed by the proximity of U.S. elections, and geopolitical conflicts elsewhere (India-China, potential sanctions against Russia/Belarus) weighing on risk sentiment.

ⁱⁱⁱ  Source: U.S. Department of Labor

5

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Overview (unaudited) (cont'd)

Strategic Income Portfolio

*  Minimum Investment

**  Commenced operations on December 30, 2014.

In accordance with SEC regulations, the Fund's performance shown assumes that all recurring fees (including management fees) were deducted and all dividends and distributions were reinvested. The performance of Class A, Class C and Class IS shares will vary from the performance of Class I shares based upon their different inception dates and will be negatively impacted by additional fees assessed to those classes (where applicable).

Performance Compared to the Bloomberg Barclays U.S. Aggregate Index⁽¹⁾, the Strategic Income Blended Index⁽²⁾ and the Lipper Alternative Credit Focus Funds Index⁽³⁾

	Period Ended September 30, 2020 Total Returns(4)
				Average Annual
	One Year			Five Years			Ten Years		Since Inception(7)
Fund — Class I Shares w/o sales charges(5)		0.98	%		3.70	%		—		2.96	%
Fund — Class A Shares w/o sales charges(5)		0.62			3.33			—		2.61
Fund — Class A Shares with maximum 3.25% sales charges(5)		–2.66			2.64			—		2.01
Fund — Class C Shares w/o sales charges(6)		–0.13			2.58			—		1.86
Fund — Class C Shares with maximum 1.00% deferred sales charges(6)		–1.11			2.58			—		1.86
Fund — Class IS Shares w/o sales charges(5)		0.89			3.75			—		3.01
Bloomberg Barclays U.S. Aggregate Index		6.98			4.18			—		3.84
Strategic Income Blended Index		6.82			2.32			—		2.02
Lipper Alternative Credit Focus Funds Index		0.47			2.64			—		2.04

Performance data quoted represents past performance, which is no guarantee of future results, and current performance may be lower or higher than the figures shown. Performance assumes that all dividends and distributions, if any, were reinvested. For the most recent month-end performance figures, please visit www.morganstanley.com/im/shareholderreports. Investment returns and principal value will fluctuate so that Fund shares, when redeemed, may be worth more or less than their original cost. Total returns do not reflect the deduction of taxes that a shareholder would pay on Fund distributions or the redemption of Fund shares. Performance of share classes will vary due to differences in sales charges and expenses.

⁽¹⁾  The Bloomberg Barclays U.S. Aggregate Index tracks the performance of U.S. government agency and Treasury securities, investment-grade corporate debt securities, agency mortgage-backed securities, asset-backed securities and commercial mortgage-backed securities. The Index is unmanaged and its returns do not include any sales charges or fees. Such costs would lower performance. It is not possible to invest directly in an index.

⁽²⁾  The Strategic Income Blended Index is a performance linked benchmark of the old and new benchmark of the Fund. The old benchmark represented by ICE BofA 3-Month U.S. Treasury Bill Index (benchmark that tracks the performance of U.S. Treasury bills with a remaining maturity of three months) from Fund's inception to September 30, 2019 and the new benchmark represented by Bloomberg Barclays U.S. Aggregate Index for periods thereafter. The Index is unmanaged and its returns do not include any sales charges or fees. Such costs would lower performance. It is not possible to invest directly in an index.

6

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Overview (unaudited) (cont'd)

Strategic Income Portfolio

⁽³⁾  The Lipper Alternative Credit Focus Funds Index is an equally weighted performance index of the largest qualifying funds (based on net assets) in the Lipper Alternative Credit Focus Funds classification. The Index, which is adjusted for capital gains distributions and income dividends, is unmanaged and should not be considered an investment. There are currently 30 funds represented in this Index. As of the date of this report, the Fund was in the Lipper Alternative Credit Focus Funds classification.

⁽⁴⁾  Total returns for the Fund reflect expenses waived and/or reimbursed, if applicable, by the Adviser. Without such waivers and/or reimbursements, total returns would have been lower.

⁽⁵⁾  Commenced operations on December 30, 2014.

⁽⁶⁾  Commenced offering on April 30, 2015.

⁽⁷⁾  For comparative purposes, average annual since inception returns listed for the Indexes refer to the inception date of Class I of the Fund, not the inception of the Indexes.

7

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments

Strategic Income Portfolio

	Face Amount (000)		Value (000)
Fixed Income Securities (97.6%)
Asset-Backed Securities (31.7%)
Aegis Asset Backed Securities Trust Mortgage Pass-Through Certificates,
1 Month USD LIBOR + 1.73%, 1.87%, 10/25/34 (a)	$	39	$	38
American Homes 4 Rent Trust,
5.64%, 4/17/52 (b)		100		111
Ameriquest Mortgage Securities, Inc.,
1 Month USD LIBOR + 2.10%, 2.25%, 5/25/34 (a)		222		224
AMSR Trust,
3.87%, 1/19/39 (a)(b)		200		201
Bayview Financial Revolving Asset Trust,
1 Month USD LIBOR + 0.93%, 1.07%, 2/28/40 (a)(b)		116		109
BCMSC Trust,
7.51%, 1/15/29 (a)		123		118
Cascade Funding Mortgage Trust,
3.40%, 4/25/30 (a)(b)		83		84
4.49%, 12/25/29 (a)(b)		205		163
CFMT 2020-HB3 LLC,
4.08%, 5/25/30 (a)(b)		200		202
Chase Funding Loan Acquisition Trust,
5.50%, 8/25/34		29		30
Conn's Receivables Funding LLC,
3.62%, 6/17/24 (b)		100		99
4.60%, 6/17/24 (b)		400		393
Consumer Loan Underlying Bond Credit Trust,
3.48%, 12/15/26 (b)		100		101
Credit-Based Asset Servicing & Securitization LLC,
1 Month USD LIBOR + 0.75%, 0.90%, 2/25/33 (a)		59		57
1 Month USD LIBOR + 1.46%, 1.60%, 5/25/32 (a)		33		34
DT Auto Owner Trust,
5.33%, 11/17/25 (b)		100		104
ECAF I Ltd.,
4.95%, 6/15/40 (b)		235		211
EquiFirst Mortgage Loan Trust,
1 Month USD LIBOR + 2.18%, 2.32%, 10/25/34 (a)		44		45
European Residential Loan Securitisation,
1 Month EURIBOR + 2.00%, 1.47%, 7/24/54 (a)	EUR	232		245
Falcon Aerospace Ltd.,
3.60%, 9/15/39 (b)	$	200		185
Finance of America HECM Buyout,
2.72%, 2/25/30 (a)(b)		200		182
3.09%, 7/25/30 (a)(b)		100		101
3.50%, 12/27/49 (b)		200		202

	Face Amount (000)		Value (000)
Financial Asset Securities Corp.,
1 Month USD LIBOR + 0.38%, 0.53%, 2/27/35 (a)(b)	$	19	$	18
FREED ABS Trust,
3.19%, 11/18/26 (b)		100		99
Goodgreen Trust,
2.63%, 4/15/55 (b)		200		202
GSAA Home Equity Trust,
6.00%, 11/25/36		23		13
GSAMP Trust,
1 Month USD LIBOR + 0.32%, 0.47%, 3/25/46 (a)		100		98
Home Partners of America Trust,
1 Month USD LIBOR + 2.65%, 2.80%, 7/17/34 (a)(b)		100		101
3.60%, 9/17/39 (b)		96		93
Invitation Homes Trust,
1 Month USD LIBOR + 2.20%, 2.35%, 1/17/38 (a)(b)		252		252
Loanpal Solar Loan 2020-2 Ltd.,
2.75%, 7/20/47 (b)		194		199
MACH 1 Cayman Ltd.,
3.47%, 10/15/39 (b)		232		213
MFA LLC,
4.16%, 7/25/48 (b)		110		110
Mosaic Solar Loan Trust,
2.10%, 4/20/46 (b)		190		195
Nationstar Home Equity Loan Trust,
1 Month USD LIBOR + 0.25%, 0.40%, 4/25/37 (a)		8		8
Newday Funding PLC,
1 Month GBP LIBOR + 2.40%, 2.46%, 9/15/27 (a)(b)	GBP	100		126
Newtek Small Business Loan Trust,
1 Month USD LIBOR + 1.70%, 1.85%, 2/25/44 (a)(b)	$	141		138
NRZ Excess Spread-Collateralized Notes,
5.44%, 6/25/25 (b)		92		93
OnDeck Asset Securitization Trust II LLC,
3.14%, 11/18/24 (b)		200		190
Ownit Mortgage Loan Trust,
1 Month USD LIBOR + 0.27%, 0.42%, 3/25/37 (a)		47		46
PNMAC GMSR Issuer Trust,
1 Month USD LIBOR + 2.65%, 2.80%, 8/25/25 (a)(b)		200		193
1 Month USD LIBOR + 2.85%, 3.00%, 2/25/23 (a)(b)		250		246
Progress Residential Trust,
3.68%, 10/17/36 (b)		200		205
4.38%, 3/17/35 (b)		100		102
Prosper Marketplace Issuance Trust,
5.50%, 10/15/24 (b)		100		99

The accompanying notes are an integral part of the financial statements.
8

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Strategic Income Portfolio

	Face Amount (000)		Value (000)
Asset-Backed Securities (cont'd)
ReadyCap Lending Small Business Loan Trust,
Daily U.S. Prime Rate –0.50%, 2.75%, 12/27/44 (a)(b)	$	83	$	77
Republic FInance Issuance Trust,
3.93%, 11/22/27 (b)		100		99
SFS Asset Securitization LLC,
4.24%, 6/10/25 (b)		153		153
Skopos Auto Receivables Trust,
3.63%, 9/16/24 (b)		100		102
SLM Student Loan Trust,
3 Month EURIBOR + 0.55%, 0.10%, 1/25/40 (a)	EUR	300		313
Small Business Origination Loan Trust,
3.85%, 12/15/27 (a)	GBP	72		51
Sprite Ltd.,
4.25%, 12/15/37 (b)	$	161		147
Stanwich Mortgage Loan Trust,
3.48%, 11/16/24 (b)		209		208
START Ireland,
4.09%, 3/15/44 (b)		165		155
Tricon American Homes Trust,
5.10%, 1/17/36 (b)		200		208
5.77%, 11/17/33 (b)		200		199
Truman Capital Mortgage Loan Trust,
1 Month USD LIBOR + 2.55%, 2.70%, 1/25/34 (a)(b)		33		33
1 Month USD LIBOR + 2.78%, 2.95%, 11/25/31 (a)(b)		36		35
Upgrade Receivables Trust,
3.51%, 10/15/25 (b)		100		101
VCAT LLC,
3.57%, 11/25/49 (a)(b)		83		83
				8,242
Collateralized Mortgage Obligation — Agency Collateral Series (0.0%)
Government National Mortgage Association, IO
0.77%, 8/20/58 (a)		306		7
Commercial Mortgage-Backed Securities (4.8%)
BX Trust,
1 Month USD LIBOR + 3.15%, 3.30%, 7/15/34 (a)(b)		85		84
GS Mortgage Securities Corp. Trust,
1 Month USD LIBOR + 2.20%, 2.35%, 10/15/36 (a)(b)		100		92
GS Mortgage Securities Trust,
4.47%, 2/10/48 (a)(b)		100		85
4.85%, 6/10/47 (a)		50		49
MFT Trust,
3.39%, 8/10/40 (a)(b)		180		181
3.48%, 2/10/42 (a)(b)		250		233
MKT 2020-525M Mortgage Trust,
2.94%, 2/12/40 (a)(b)		250		227

	Face Amount (000)		Value (000)
Multifamily Connecticut Avenue Securities Trust,
1 Month USD LIBOR + 1.70%, 1.85%, 10/15/49 (a)(b)	$	95	$	91
Natixis Commercial Mortgage Securities Trust,
4.30%, 10/15/36 (b)		150		141
Wells Fargo Commercial Mortgage Trust,
4.28%, 5/15/48 (a)		75		71
				1,254
Corporate Bonds (43.4%)
Communications (0.2%)
TEGNA, Inc.,
4.63%, 3/15/28 (b)		45		44
Finance (23.3%)
ABN Amro Bank N.V.,
4.75%, 7/28/25 (b)		200		226
Aon Corp.,
2.20%, 11/15/22		50		52
Avolon Holdings Funding Ltd.,
2.88%, 2/15/25 (b)		50		46
Bank of America Corp.,
2.46%, 10/22/25		250		264
4.25%, 10/22/26		350		406
Barclays PLC,
2.85%, 5/7/26		200		208
Belrose Funding Trust,
2.33%, 8/15/30 (b)		125		124
BNP Paribas SA,
1.13%, 6/11/26	EUR	100		122
Brown & Brown, Inc.,
2.38%, 3/15/31	$	75		76
4.20%, 9/15/24		50		55
Citigroup, Inc.,
1.68%, 5/15/24		250		256
5.50%, 9/13/25		325		386
CNO Financial Group, Inc.,
5.25%, 5/30/29		125		145
Cooperatieve Rabobank UA,
2.50%, 5/26/26	EUR	100		119
Credit Agricole SA,
1.38%, 3/13/25		100		123
Crown Castle International Corp.,
3.30%, 7/1/30		25		27
CyrusOne LP/CyrusOne Finance Corp.,
2.90%, 11/15/24	$	25		26
DBS Group Holdings Ltd.,
1.50%, 4/11/28	EUR	100		119
Deutsche Bank AG,
3.15%, 1/22/21	$	100		101
Discover Financial Services,
3.95%, 11/6/24		25		27
Equitable Holdings, Inc.,
3.90%, 4/20/23		250		269

The accompanying notes are an integral part of the financial statements.
9

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Strategic Income Portfolio

	Face Amount (000)		Value (000)
Finance (cont'd)
ERP Operating LP,
4.15%, 12/1/28	$	100	$	119
Goldman Sachs Group, Inc. (The),
2.00%, 11/1/28	EUR	100		130
4.25%, 10/21/25	$	125		142
Intesa Sanpaolo SpA,
6.50%, 2/24/21 (b)		125		128
Iron Mountain, Inc.,
4.88%, 9/15/29 (b)		75		76
Itau Unibanco Holding SA,
2.90%, 1/24/23 (b)		250		253
Kimco Realty Corp.,
2.70%, 10/1/30		125		127
LeasePlan Corp.,
2.88%, 10/24/24 (b)		200		207
Macquarie Bank Ltd.,
2.10%, 10/17/22 (b)		150		155
Metropolitan Life Global Funding I,
0.95%, 7/2/25 (b)		150		151
PNC Financial Services Group, Inc. (The),
2.20%, 11/1/24		225		238
Post Holdings, Inc.,
5.50%, 12/15/29 (b)		25		27
Prologis LP,
1.25%, 10/15/30		150		147
Shinhan Financial Group Co. Ltd.,
1.35%, 1/10/26 (b)		200		200
SVB Financial Group,
3.13%, 6/5/30		50		56
Synchrony Financial,
4.25%, 8/15/24		250		272
Transurban Finance Co. Pty Ltd.,
2.45%, 3/16/31 (b)		100		102
USAA Capital Corp.,
1.50%, 5/1/23 (b)		150		154
Visa, Inc.,
0.75%, 8/15/27		75		75
Vonovia Finance BV,
4.00%, 12/17/21 (c)	EUR	100		122
				6,058
Industrials (18.3%)
AbbVie, Inc.,
2.95%, 11/21/26 (b)	$	175		191
3.60%, 5/14/25		125		139
Albertsons Cos., Inc./Safeway, Inc./ New Albertson's, Inc./Albertson's LLC,
5.75%, 3/15/25		20		21
Alphabet, Inc.,
1.10%, 8/15/30		125		125
American Axle & Manufacturing, Inc.,
6.50%, 4/1/27		75		73
Aviation Capital Group LLC,
4.38%, 1/30/24 (b)		250		249

	Face Amount (000)		Value (000)
Avis Budget Car Rental LLC/Avis Budget Finance, Inc.,
5.75%, 7/15/27 (b)	$	49	$	44
Berry Global, Inc.,
4.50%, 2/15/26 (b)		25		25
Boyd Gaming Corp.,
4.75%, 12/1/27		40		39
CSX Corp.,
2.40%, 2/15/30		75		81
Diamond Sports Group LLC/Diamond Sports Finance Co.,
6.63%, 8/15/27 (b)		75		39
Ford Motor Credit Co., LLC,
3.10%, 5/4/23		200		196
Garda World Security Corp.,
9.50%, 11/1/27 (b)		50		53
Global Partners LP/GLP Finance Corp.,
7.00%, 6/15/23 - 8/1/27		75		77
Grifols SA,
2.25%, 11/15/27 (b)	EUR	100		117
Grinding Media, Inc./Moly-Cop AltaSteel Ltd.,
7.38%, 12/15/23 (b)	$	75		76
Hanesbrands, Inc.,
4.88%, 5/15/26 (b)		75		80
HCA, Inc.,
4.13%, 6/15/29		125		141
Hudbay Minerals, Inc.,
7.63%, 1/15/25 (b)		75		76
Johnson Controls International plc/Tyco Fire & Security Finance SCA,
1.75%, 9/15/30		50		50
Koppers, Inc.,
6.00%, 2/15/25 (b)		75		76
Level 3 Financing, Inc.,
3.40%, 3/1/27 (b)		225		243
Lions Gate Capital Holdings LLC,
5.88%, 11/1/24 (b)		25		25
Mauser Packaging Solutions Holding Co.,
7.25%, 4/15/25 (b)		25		24
MDC Partners, Inc.,
6.50%, 5/1/24 (b)		75		69
Mosaic Co. (The),
4.25%, 11/15/23		125		136
Navistar International Corp.,
6.63%, 11/1/25 (b)		75		77
NortonLifeLock, Inc.,
5.00%, 4/15/25 (b)		75		77
NXP BV/NXP Funding LLC/NXP USA, Inc.,
3.40%, 5/1/30 (b)		125		137
Oceaneering International, Inc.,
6.00%, 2/1/28		75		47
Q-Park Holding I BV,
1.50%, 3/1/25 (b)	EUR	100		107

The accompanying notes are an integral part of the financial statements.
10

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Strategic Income Portfolio

	Face Amount (000)		Value (000)
Industrials (cont'd)
Rockies Express Pipeline LLC,
3.60%, 5/15/25 (b)	$	75	$	74
Royalty Pharma PLC,
1.20%, 9/2/25 (b)		125		125
Sabine Pass Liquefaction LLC,
4.20%, 3/15/28		130		141
Sally Holdings LLC/Sally Capital, Inc.,
5.63%, 12/1/25		75		76
Select Medical Corp.,
6.25%, 8/15/26 (b)		75		78
Silgan Holdings, Inc.,
2.25%, 6/1/28	EUR	100		115
Sotheby's,
7.38%, 10/15/27 (b)		200		200
Sprint Spectrum Co., LLC/Sprint Spectrum Co., II LLC/Sprint Spectrum Co., III LLC,
4.74%, 9/20/29 (b)		200		217
Standard Industries, Inc.,
2.25%, 11/21/26 (b)	EUR	100		112
Thermo Fisher Scientific, Inc.,
4.13%, 3/25/25	$	325		370
Verizon Communications, Inc.,
3.88%, 2/8/29		200		237
Western Midstream Operating LP,
4.10%, 2/1/25		75		72
Wolverine World Wide, Inc.,
5.00%, 9/1/26 (b)		25		25
				4,752
Utilities (1.6%)
Greenko Investment Co.,
4.88%, 8/16/23		200		200
Liberty Utilities Finance GP 1,
2.05%, 9/15/30 (b)		100		99
ONEOK, Inc.,
3.40%, 9/1/29		125		123
				422
				11,276
Mortgages — Other (13.3%)
Alba PLC,
3 Month GBP LIBOR + 0.50%, 0.55%, 3/17/39 (a)	GBP	33		38
Alternative Loan Trust,
4.15%, 3/25/35 (a)	$	23		23
5.75%, 3/25/34		32		32
PAC
1 Month USD LIBOR + 0.45%, 0.60%, 10/25/36 (a)		37		16
Banc of America Alternative Loan Trust,
5.71%, 10/25/36 (a)		69		31
Banc of America Mortgage Trust,
3.21%, 6/25/35 (a)		110		107
4.37%, 3/25/33 (a)		20		19

	Face Amount (000)		Value (000)
Bear Stearns ARM Trust,
2.77%, 8/25/33 (a)	$	118	$	117
3.25%, 2/25/36 (a)		26		25
Bear Stearns Trust,
3.06%, 4/25/35 (a)		27		22
Cascade Funding Mortgage Trust,
2.80%, 6/25/69 (a)(b)		173		174
4.00%, 10/25/68 (a)(b)		225		220
5.80%, 6/25/48 (b)		100		99
Citigroup Mortgage Loan Trust,
3.35%, 6/25/36 (a)		23		13
Deephaven Residential Mortgage Trust,
3.49%, 12/26/46 (a)(b)		79		80
E-MAC Program BV,
3 Month EURIBOR + 0.17%, 1.51%, 4/25/39 (a)	EUR	65		64
Eurohome Mortgages PLC,
3 Month EURIBOR + 0.21%, 0.00%, 8/2/50 (a)		19		20
FMC GMSR Issuer Trust,
5.07%, 5/25/24 (a)(b)	$	200		203
Galton Funding Mortgage Trust,
4.00%, 2/25/59 (a)(b)		42		43
GC Pastor Hipotecario 5 FTA,
3 Month EURIBOR + 0.17%, 0.00%, 6/21/46 (a)	EUR	33		35
Grifonas Finance PLC,
6 Month EURIBOR + 0.28%, 0.00%, 8/28/39 (a)		60		68
GSR Mortgage Loan Trust,
3.86%, 12/25/34 (a)	$	42		42
HarborView Mortgage Loan Trust,
3.16%, 6/19/34 (a)		57		59
3.35%, 2/25/36 (a)		27		14
Hipocat 11 FTA,
3 Month EURIBOR + 0.13%, 0.00%, 1/15/50 (a)	EUR	19		21
IM Pastor 3 FTH,
3 Month EURIBOR + 0.14%, 0.00%, 3/22/43 (a)		65		69
IM Pastor 4 FTA,
3 Month EURIBOR + 0.14%, 0.00%, 3/22/44 (a)		55		59
IndyMac INDX Mortgage Loan Trust,
3.72%, 12/25/34 (a)	$	19		19
Lansdowne Mortgage Securities No. 1 PLC,
3 Month EURIBOR + 0.30%, 0.00%, 6/15/45 (a)	EUR	13		14
Lansdowne Mortgage Securities No. 2 PLC,
3 Month EURIBOR + 0.34%, 0.00%, 9/16/48 (a)		38		40
Lehman Mortgage Trust,
6.00%, 7/25/36	$	56		40

The accompanying notes are an integral part of the financial statements.
11

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Strategic Income Portfolio

	Face Amount (000)		Value (000)
Mortgages — Other (cont'd)
LHOME Mortgage Trust,
3.87%, 7/25/24 (b)	$	100	$	101
National City Mortgage Capital Trust,
6.00%, 3/25/38		11		12
Newgate Funding PLC,
3 Month GBP LIBOR + 3.00%, 3.06%, 12/15/50 (a)	GBP	111		136
OBX Trust,
3.50%, 10/25/59 (a)(b)	$	67		69
PMC PLS ESR Issuer LLC,
5.07%, 11/25/24 (b)		114		112
PRPM LLC,
3.50%, 10/25/24 (a)(b)		87		87
RBSSP Resecuritization Trust,
3.32%, 12/25/35 (a)(b)		112		112
Reperforming Loan REMIC Trust,
8.50%, 6/25/35 (b)		42		46
ResLoC UK PLC,
3 Month EURIBOR + 0.45%, 0.00%, 12/15/43 (a)	EUR	100		101
Seasoned Credit Risk Transfer Trust,
3.75%, 9/25/55 (a)(b)	$	150		148
4.75%, 5/25/57 (a)		100		98
4.75%, 7/25/58 (a)(b)		200		197
Silver Hill Trust,
3.10%, 11/25/49 (a)(b)		132		135
STARM Mortgage Loan Trust,
3.70%, 1/25/37 (a)		15		15
Uropa Securities PLC,
3 Month GBP LIBOR + 0.55%, 0.61%, 6/10/59 (a)	GBP	79		93
3 Month GBP LIBOR + 0.55%, 0.64%, 10/10/40 (a)		87		95
3 Month GBP LIBOR + 0.75%, 0.81%, 6/10/59 (a)		36		43
Washington Mutual MSC Mortgage Pass- Through Certificates,
5.50%, 3/25/33	$	20		21
				3,447
Sovereign (4.4%)
Australia Government Bond,
2.75%, 11/21/28	AUD	1		1
Brazil Notas do Tesouro Nacional Series F,
10.00%, 1/1/29	BRL	300		62
Ghana Government International Bond,
8.13%, 1/18/26	$	200		201
Guatemala Government Bond,
4.88%, 2/13/28		200		221
Hellenic Republic Government Bond,
3.38%, 2/15/25 (b)	EUR	115		152
3.45%, 4/2/24 (b)		40		52
Indonesia Treasury Bond,
6.13%, 5/15/28	IDR	635,000		41
8.25%, 5/15/29		465,000		34

	Face Amount (000)		Value (000)
Peruvian Government International Bond, (Units)
5.40%, 8/12/34 (b)(d)	PEN	60	$	17
Senegal Government International Bond,
6.25%, 5/23/33	$	200		198
Ukraine Government International Bond,
7.75%, 9/1/23		150		153
				1,132
Total Fixed Income Securities (Cost $25,338)				25,358
	Shares
Short-Term Investments (1.5%)
Investment Company (0.5%)
Morgan Stanley Institutional Liquidity Funds — Government Portfolio — Institutional Class (See Note G) (Cost $118)		117,638		118
	Face Amount (000)
U.S. Treasury Security (1.0%)
U.S. Treasury Bill
0.16%, 1/28/21 (e)(f) (Cost $255)	$	255		255
Total Short-Term Investments (Cost $373)				373
Total Investments (99.1%) (Cost $25,711) (g)(h)				25,731
Other Assets in Excess of Liabilities (0.9%)				234
Net Assets (100.0%)			$	25,965

(a)  Floating or variable rate securities: The rates disclosed are as of September 30, 2020. For securities based on a published reference rate and spread, the reference rate and spread are indicated in the description in the Portfolio of Investments. Certain variable rate securities may not be based on a published reference rate and spread but are determined by the issuer or agent and are based on current market conditions. These securities do not indicate a reference rate and spread in their description in the Portfolio of Investments.

(b)  144A security — Certain conditions for public sale may exist. Unless otherwise noted, these securities are deemed to be liquid.

(c)  Perpetual — One or more securities do not have a predetermined maturity date. Rates for these securities are fixed for a period of time, after which they revert to a floating rate. Interest rates in effect are as of September 30, 2020.

(d)  Consists of one or more classes of securities traded together as a unit.

(e)  Rate shown is the yield to maturity at September 30, 2020.

(f)  All or a portion of the security was pledged to cover margin requirements for swap agreements.

(g)  Securities are available for collateral in connection with open foreign currency forward exchange contracts, futures contracts and swap agreement.

(h)  At September 30, 2020, the aggregate cost for federal income tax purposes is approximately $25,825,000. The aggregate gross unrealized appreciation is approximately $547,000 and the aggregate gross unrealized depreciation is approximately $533,000, resulting in net unrealized appreciation of approximately $14,000.

EURIBOR  Euro Interbank Offered Rate.

IO  Interest Only.

LIBOR  London Interbank Offered Rate.

PAC  Planned Amortization Class.

REMIC  Real Estate Mortgage Investment Conduit.

The accompanying notes are an integral part of the financial statements.
12

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Strategic Income Portfolio

Foreign Currency Forward Exchange Contracts:

The Fund had the following foreign currency forward exchange contracts open at September 30, 2020:

Counterparty	Contracts to Deliver (000)		In Exchange For (000)		Delivery Date	Unrealized Appreciation (Depreciation) (000)
Australia and New Zealand Banking Group	GBP	489	$	646	12/1/20	$	15
Barclays Bank PLC	$	7	GBP	6	12/1/20		—	@
Citibank NA	EUR	2,222	$	2,648	12/1/20		40
Citibank NA	$	131	EUR	110	12/1/20		(1	)
JPMorgan Chase Bank NA	BRL	367	$	65	12/1/20		—	@
JPMorgan Chase Bank NA	IDR	1,132,494	$	76	12/1/20		1
JPMorgan Chase Bank NA	PEN	65	$	18	12/1/20		—	@
UBS AG	$	12	EUR	10	12/1/20		—	@
						$	55

Futures Contracts:

The Fund had the following futures contracts open at September 30, 2020:

	Number of Contracts		Expiration Date	Notional Amount (000)			Value (000)			Unrealized Depreciation (000)
Short:
U.S. Treasury 10 yr. Ultra Long Bond (United States)		3	Dec-20	$	(300	)	$	(480	)	$	(1	)
U.S. Treasury 10 yr. Note (United States)		1	Dec-20		(100	)		(140	)		(—	@)
U.S. Treasury 5 yr. Note (United States)		12	Dec-20		(1,200	)		(1,512	)		(3	)
German Euro Bund (Germany)		2	Dec-20	EUR	(200	)		(409	)		(3	)
										$	(7	)

Credit Default Swap Agreement:

The Fund had the following credit default swap agreement open at September 30, 2020:

Swap Counterparty and Reference Obligation	Credit Rating of Reference Obligation†	Buy/Sell Protection	Pay/Receive Fixed Rate			Payment Frequency	Maturity Date	Notional Amount (000)		Value (000)		Upfront Payment Received (000)			Unrealized Appreciation (000)
Morgan Stanley & Co. LLC* CDX.NA.HY.34	NR	Sell		5.00	%	Monthly	6/20/25	$	1,219	$	61	$	(54	)	$	115

@  —  Value is less than $500.

†  —  Credit rating as issued by Standard & Poor's.

*  —  Cleared swap agreement, the broker is Morgan Stanley & Co. LLC.

NR  —  Not rated.

AUD  —  Australian Dollar

BRL  —  Brazilian Real

EUR  —  Euro

GBP  —  British Pound

IDR  —  Indonesian Rupiah

PEN  —  Peruvian Nuevo Sol

USD  —  United States Dollar

Portfolio Composition

Classification	Percentage of Total Investments
Asset-Backed Securities		32.0	%
Finance		23.5
Industrials		18.5
Mortgages — Other		13.4
Other**		11.1
Short-Term Investments		1.5
Total Investments		100.0	%***

**  Industries and/or investment types representing less than 5% of total investments.

***  Does not include open short futures contracts with a value of approximately $2,541,000 and with total unrealized depreciation of approximately $7,000. Does not include open foreign currency forward exchange contracts with net unrealized appreciation of approximately $55,000 Does not include open swap agreements with total unrealized appreciation of approximately $115,000.

The accompanying notes are an integral part of the financial statements.
13

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Strategic Income Portfolio

Statement of Assets and Liabilities	September 30, 2020 (000)
Assets:
Investments in Securities of Unaffiliated Issuers, at Value (Cost $25,593)	$	25,613
Investment in Security of Affiliated Issuer, at Value (Cost $118)		118
Total Investments in Securities, at Value (Cost $25,711)		25,731
Foreign Currency, at Value (Cost $5)		5
Interest Receivable		143
Due from Adviser		78
Unrealized Appreciation on Foreign Currency Forward Exchange Contracts		56
Receivable for Variation Margin on Futures Contracts		28
Receivable for Variation Margin on Swap Agreements		2
Tax Reclaim Receivable		1
Receivable for Investments Sold		—	@
Receivable from Affiliate		—	@
Other Assets		22
Total Assets		26,066
Liabilities:
Payable for Professional Fees		72
Payable for Custodian Fees		9
Payable for Transfer Agency Fees — Class I		1
Payable for Transfer Agency Fees — Class A		1
Payable for Transfer Agency Fees — Class C		1
Payable for Transfer Agency Fees — Class IS		1
Payable for Administration Fees		2
Unrealized Depreciation on Foreign Currency Forward Exchange Contracts		1
Deferred Capital Gain Country Tax		1
Payable for Shareholder Services Fees — Class A		—	@
Payable for Distribution and Shareholder Services Fees — Class C		—	@
Payable for Sub Transfer Agency Fees — Class A		—	@
Payable for Sub Transfer Agency Fees — Class C		—	@
Other Liabilities		12
Total Liabilities		101
Net Assets	$	25,965
Net Assets Consist of:
Paid-in-Capital	$	26,349
Total Accumulated Loss		(384	)
Net Assets	$	25,965

The accompanying notes are an integral part of the financial statements.
14

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Strategic Income Portfolio

Statement of Assets and Liabilities (cont'd)	September 30, 2020 (000)
CLASS I:
Net Assets	$	15,145
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		1,527,960
Net Asset Value, Offering and Redemption Price Per Share	$	9.91
CLASS A:
Net Assets	$	204
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		20,643
Net Asset Value, Redemption Price Per Share	$	9.90
Maximum Sales Load		3.25	%
Maximum Sales Charge	$	0.33
Maximum Offering Price Per Share	$	10.23
CLASS C:
Net Assets	$	266
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		26,997
Net Asset Value, Offering and Redemption Price Per Share	$	9.87
CLASS IS:
Net Assets	$	10,350
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		1,043,918
Net Asset Value, Offering and Redemption Price Per Share	$	9.91

@  Amount is less than $500.

The accompanying notes are an integral part of the financial statements.
15

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Strategic Income Portfolio

Statement of Operations	Year Ended September 30, 2020 (000)
Investment Income:
Interest from Securities of Unaffiliated Issuers (Net of $2 of Foreign Taxes Withheld)	$	855
Dividends from Security of Affiliated Issuer (Note G)		5
Total Investment Income		860
Expenses:
Professional Fees		242
Advisory Fees (Note B)		81
Registration Fees		56
Custodian Fees (Note F)		31
Pricing Fees		23
Shareholder Reporting Fees		22
Administration Fees (Note C)		20
Transfer Agency Fees — Class I (Note E)		2
Transfer Agency Fees — Class A (Note E)		2
Transfer Agency Fees — Class C (Note E)		2
Transfer Agency Fees — Class IS (Note E)		2
Trustees' Fees and Expenses		5
Shareholder Services Fees — Class A (Note D)		1
Distribution and Shareholder Services Fees — Class C (Note D)		2
Sub Transfer Agency Fees — Class I		—	@
Sub Transfer Agency Fees — Class A		—	@
Sub Transfer Agency Fees — Class C		—	@
Other Expenses		21
Total Expenses		512
Expenses Reimbursed by Adviser (Note B)		(273	)
Waiver of Advisory Fees (Note B)		(81	)
Reimbursement of Class Specific Expenses — Class A (Note B)		(2	)
Reimbursement of Class Specific Expenses — Class C (Note B)		(2	)
Reimbursement of Class Specific Expenses — Class IS (Note B)		(2	)
Rebate from Morgan Stanley Affiliate (Note G)		(1	)
Net Expenses		151
Net Investment Income		709
Realized Gain (Loss):
Investments Sold		106
Foreign Currency Forward Exchange Contracts		(141	)
Foreign Currency Translation		(2	)
Futures Contracts		(61	)
Options Written		15
Swap Agreements		(257	)
Net Realized Loss		(340	)
Change in Unrealized Appreciation (Depreciation):
Investments (Net of Increase in Deferred Capital Gain Country Tax of $1)		(243	)
Foreign Currency Forward Exchange Contracts		14
Foreign Currency Translation		3
Futures Contracts		(12	)
Swap Agreements		117
Net Change in Unrealized Appreciation (Depreciation)		(121	)
Net Realized Loss and Change in Unrealized Appreciation (Depreciation)		(461	)
Net Increase in Net Assets Resulting from Operations	$	248

@  Amount is less than $500.

The accompanying notes are an integral part of the financial statements.
16

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Strategic Income Portfolio

Statements of Changes in Net Assets	Year Ended September 30, 2020 (000)			Year Ended September 30, 2019 (000)
Increase (Decrease) in Net Assets:
Operations:
Net Investment Income	$	709		$	275
Net Realized Loss		(340	)		(35	)
Net Change in Unrealized Appreciation (Depreciation)		(121	)		140
Net Increase in Net Assets Resulting from Operations		248			380
Dividends and Distributions to Shareholders:
Class I		(439	)		(1	)
Class A		(12	)		(6	)
Class C		(3	)		(1	)
Class IS		(301	)		(595	)
Total Dividends and Distributions to Shareholders		(755	)		(603	)
Capital Share Transactions:(1)
Class I:
Subscribed		15,041			—
Distributions Reinvested		439			—	@
Redeemed		(40	)		—
Class A:
Subscribed		1,505			216
Distributions Reinvested		12			6
Redeemed		(1,529	)		(72	)
Class C:
Subscribed		257			36
Distributions Reinvested		3			1
Redeemed		(47	)		(5	)
Class IS:
Distributions Reinvested		301			153
Net Increase in Net Assets Resulting from Capital Share Transactions		15,942			335
Total Increase in Net Assets		15,435			112
Net Assets:
Beginning of Period		10,530			10,418
End of Period	$	25,965		$	10,530
(1)   Capital Share Transactions:
Class I:
Shares Subscribed		1,487			—
Shares Issued on Distributions Reinvested		45			—	@@
Shares Redeemed		(5	)		—
Net Increase in Class I Shares Outstanding		1,527			—	@@
Class A:
Shares Subscribed		152			21
Shares Issued on Distributions Reinvested		1			1
Shares Redeemed		(155	)		(7	)
Net Increase (Decrease) in Class A Shares Outstanding		(2	)		15
Class C:
Shares Subscribed		27			4
Shares Issued on Distributions Reinvested		—	@@		—	@@
Shares Redeemed		(5	)		(1	)
Net Increase in Class C Shares Outstanding		22			3
Class IS:
Shares Issued on Distributions Reinvested		31			15

@  Amount is less than $500.

@@  Amount is less than 500 shares.

The accompanying notes are an integral part of the financial statements.
17

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Strategic Income Portfolio

	Class I
	Year Ended September 30,
Selected Per Share Data and Ratios	2020			2019			2018			2017			2016(1)
Net Asset Value, Beginning of Period	$	10.11		$	10.33		$	10.21		$	9.69		$	9.79
Income (Loss) from Investment Operations:
Net Investment Income(2)		0.27			0.26			0.28			0.26			0.22
Net Realized and Unrealized Gain (Loss)		(0.18	)		0.10			0.05			0.47			0.06
Total from Investment Operations		0.09			0.36			0.33			0.73			0.28
Distributions from and/or in Excess of:
Net Investment Income		(0.29	)		(0.44	)		(0.21	)		(0.21	)		(0.38	)
Net Realized Gain		—			(0.14	)		—			—			—
Total Distributions		(0.29	)		(0.58	)		(0.21	)		(0.21	)		(0.38	)
Net Asset Value, End of Period	$	9.91		$	10.11		$	10.33		$	10.21		$	9.69
Total Return(3)		0.98	%		3.79	%		3.32	%		7.64	%		2.91	%
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	15,145		$	10		$	10		$	10		$	10
Ratio of Expenses Before Expense Limitation		1.98	%		24.26	%		25.49	%		21.19	%		7.28	%
Ratio of Expenses After Expense Limitation		0.58	%(4)(5)		0.99	%(4)		0.99	%(4)		0.99	%(4)		0.99	%(4)
Ratio of Net Investment Income		2.81	%(4)		2.61	%(4)		2.77	%(4)		2.63	%(4)		2.25	%(4)
Ratio of Rebate from Morgan Stanley Affiliates		0.00	%(6)		0.01	%		0.01	%		0.01	%		0.01	%
Portfolio Turnover Rate		161	%		97	%		75	%		64	%		47	%

(1)  Reflects prior period custodian out-of-pocket expenses that were reimbursed in September 2016. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class I shares. The Ratio of Expenses After Expense Limitation and the Ratio of Net Investment Income would be unchanged as the reimbursement of custodian fees was offset against expense waivers/reimbursements with no impact to net expenses or net investment income.

(2)  Per share amount is based on average shares outstanding.

(3)  Calculated based on the net asset value as of the last business day of the period.

(4)  The Ratio of Expenses After Expense Limitation and Ratio of Net Investment Income reflect the rebate of certain Fund expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates."

(5)  Effective October 01, 2019, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 0.60% for Class I shares. Prior to October 01, 2019, the maximum ratio was 1.00% for Class I shares.

(6)  Amount is less than 0.005%.

The accompanying notes are an integral part of the financial statements.
18

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Strategic Income Portfolio

	Class A
	Year Ended September 30,
Selected Per Share Data and Ratios	2020			2019			2018			2017			2016(1)
Net Asset Value, Beginning of Period	$	10.09		$	10.31		$	10.20		$	9.69		$	9.79
Income (Loss) from Investment Operations:
Net Investment Income(2)		0.24			0.22			0.25			0.20			0.18
Net Realized and Unrealized Gain (Loss)		(0.17	)		0.11			0.04			0.49			0.06
Total from Investment Operations		0.07			0.33			0.29			0.69			0.24
Distributions from and/or in Excess of:
Net Investment Income		(0.26	)		(0.41	)		(0.18	)		(0.18	)		(0.34	)
Net Realized Gain		—			(0.14	)		—			—			—
Total Distributions		(0.26	)		(0.55	)		(0.18	)		(0.18	)		(0.34	)
Net Asset Value, End of Period	$	9.90		$	10.09		$	10.31		$	10.20		$	9.69
Total Return(3)		0.62	%		3.52	%		2.92	%		7.18	%		2.51	%
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	204		$	224		$	77		$	10		$	40
Ratio of Expenses Before Expense Limitation		2.89	%		4.82	%		7.09	%		9.96	%		6.73	%
Ratio of Expenses After Expense Limitation		0.95	%(4)(5)		1.34	%(4)		1.34	%(4)		1.33	%(4)		1.34	%(4)
Ratio of Net Investment Income		2.44	%(4)		2.21	%(4)		2.40	%(4)		2.08	%(4)		1.86	%(4)
Ratio of Rebate from Morgan Stanley Affiliates		0.00	%(6)		0.01	%		0.01	%		0.02	%		0.01	%
Portfolio Turnover Rate		161	%		97	%		75	%		64	%		47	%

(1)  Reflects prior period custodian out-of-pocket expenses that were reimbursed in September 2016. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class A shares. The Ratio of Expenses After Expense Limitation and the Ratio of Net Investment Income would be unchanged as the reimbursement of custodian fees was offset against expense waivers/reimbursements with no impact to net expenses or net investment income.

(2)  Per share amount is based on average shares outstanding.

(3)  Calculated based on the net asset value which does not reflect sales charges, if applicable, as of the last business day of the period.

(4)  The Ratio of Expenses After Expense Limitation and Ratio of Net Investment Income reflect the rebate of certain Fund expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates."

(5)  Effective October 01, 2019, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 0.95% for Class A shares. Prior to October 01, 2019, the maximum ratio was 1.35% for Class A shares.

(6)  Amount is less than 0.005%.

The accompanying notes are an integral part of the financial statements.
19

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Strategic Income Portfolio

	Class C
	Year Ended September 30,
Selected Per Share Data and Ratios	2020			2019			2018			2017			2016(1)
Net Asset Value, Beginning of Period	$	10.07		$	10.28		$	10.17		$	9.66		$	9.76
Income (Loss) from Investment Operations:
Net Investment Income(2)		0.16			0.14			0.17			0.13			0.11
Net Realized and Unrealized Gain (Loss)		(0.17	)		0.11			0.05			0.49			0.06
Total from Investment Operations		(0.01	)		0.25			0.22			0.62			0.17
Distributions from and/or in Excess of:
Net Investment Income		(0.19	)		(0.32	)		(0.11	)		(0.11	)		(0.27	)
Net Realized Gain		—			(0.14	)		—			—			—
Total Distributions		(0.19	)		(0.46	)		(0.11	)		(0.11	)		(0.27	)
Net Asset Value, End of Period	$	9.87		$	10.07		$	10.28		$	10.17		$	9.66
Total Return(3)		(0.13	)%		2.78	%		2.11	%		6.46	%		1.77	%
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	266		$	50		$	20		$	22		$	35
Ratio of Expenses Before Expense Limitation		4.43	%		10.78	%		14.46	%		13.41	%		28.93	%
Ratio of Expenses After Expense Limitation		1.70	%(4)(5)		2.09	%(4)		2.09	%(4)		2.09	%(4)		2.09	%(4)
Ratio of Net Investment Income		1.70	%(4)		1.45	%(4)		1.69	%(4)		1.33	%(4)		1.14	%(4)
Ratio of Rebate from Morgan Stanley Affiliates		0.00	%(6)		0.01	%		0.01	%		0.01	%		0.01	%
Portfolio Turnover Rate		161	%		97	%		75	%		64	%		47	%

(1)  Reflects prior period custodian out-of-pocket expenses that were reimbursed in September 2016. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class C shares. The Ratio of Expenses After Expense Limitation and the Ratio of Net Investment Income would be unchanged as the reimbursement of custodian fees was offset against expense waivers/reimbursements with no impact to net expenses or net investment income.

(2)  Per share amount is based on average shares outstanding.

(3)  Calculated based on the net asset value which does not reflect sales charges, if applicable, as of the last business day of the period.

(4)  The Ratio of Expenses After Expense Limitation and Ratio of Net Investment Income reflect the rebate of certain Fund expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates."

(5)  Effective October 01, 2019, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 1.70% for Class C shares. Prior to October 01, 2019, the maximum ratio was 2.10% for Class C shares.

(6)  Amount is less than 0.005%.

The accompanying notes are an integral part of the financial statements.
20

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Strategic Income Portfolio

	Class IS
	Year Ended September 30,
Selected Per Share Data and Ratios	2020			2019			2018			2017			2016(1)
Net Asset Value, Beginning of Period	$	10.11		$	10.33		$	10.22		$	9.69		$	9.79
Income (Loss) from Investment Operations:
Net Investment Income(2)		0.28			0.27			0.29			0.27			0.23
Net Realized and Unrealized Gain (Loss)		(0.19	)		0.10			0.04			0.48			0.05
Total from Investment Operations		0.09			0.37			0.33			0.75			0.28
Distributions from and/or in Excess of:
Net Investment Income		(0.29	)		(0.45	)		(0.22	)		(0.22	)		(0.38	)
Net Realized Gain		—			(0.14	)		—			—			—
Total Distributions		(0.29	)		(0.59	)		(0.22	)		(0.22	)		(0.38	)
Net Asset Value, End of Period	$	9.91		$	10.11		$	10.33		$	10.22		$	9.69
Total Return(3)		0.89	%		3.95	%		3.27	%		7.80	%		2.96	%
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	10,350		$	10,246		$	10,311		$	10,197		$	9,669
Ratio of Expenses Before Expense Limitation		1.99	%		3.06	%		3.28	%		3.79	%		3.45	%
Ratio of Expenses After Expense Limitation		0.57	%(4)(5)		0.94	%(4)		0.94	%(4)		0.94	%(4)		0.94	%(4)
Ratio of Net Investment Income		2.81	%(4)		2.66	%(4)		2.83	%(4)		2.68	%(4)		2.35	%(4)
Ratio of Rebate from Morgan Stanley Affiliates		0.00	%(6)		0.01	%		0.01	%		0.01	%		0.01	%
Portfolio Turnover Rate		161	%		97	%		75	%		64	%		47	%

(1)  Reflects prior period custodian out-of-pocket expenses that were reimbursed in September 2016. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class IS shares. The Ratio of Expenses After Expense Limitation and the Ratio of Net Investment Income would be unchanged as the reimbursement of custodian fees was offset against expense waivers/reimbursements with no impact to net expenses or net investment income.

(2)  Per share amount is based on average shares outstanding.

(3)  Calculated based on the net asset value as of the last business day of the period.

(4)  The Ratio of Expenses After Expense Limitation and Ratio of Net Investment Income reflect the rebate of certain Fund expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates."

(5)  Effective October 01, 2019, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 0.57% for Class IS shares. Prior to October 01, 2019, the maximum ratio was 0.95% for Class IS shares.

(6)  Amount is less than 0.005%.

The accompanying notes are an integral part of the financial statements.
21

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements

Morgan Stanley Institutional Fund Trust ("Trust") is registered under the Investment Company Act of 1940, as amended (the "Act''), as an open-end management investment company. The Trust is comprised of twelve separate, active funds (individually referred to as a "Fund," collectively as the "Funds"). The Trust applies investment company accounting and reporting guidance. All Funds are considered diversified for purposes of the Act.

The accompanying financial statements relate to the Strategic Income Portfolio. The Fund seeks to maximize current income consistent with the preservation of capital. The Fund offers four classes of shares — Class I, Class A, Class C and Class IS.

A. Significant Accounting Policies: The following significant accounting policies are in conformity with U.S. generally accepted accounting principles ("GAAP"). Such policies are consistently followed by the Trust in the preparation of its financial statements. GAAP may require management to make estimates and assumptions that affect the reported amounts and disclosures in the financial statements. Actual results may differ from those estimates.

In March 2017, the Financial Accounting Standards Board ("FASB") issued an Accounting Standard Update, ASU 2017-08, Receivables-Nonrefundable Fees and Other Costs (Subtopic 310-20), Premium Amortization on Purchased Callable Debt Securities ("ASU 2017-08") which amends the amortization period for certain purchased callable debt securities held at a premium, shortening such period to the earliest call date. ASU 2017-08 does not require any accounting change for debt securities held at a discount; the discount continues to be accreted to maturity. ASU 2017-08 is effective for fiscal years, and interim periods within those fiscal years, beginning after December 15, 2018. The adoption resulted in a change in accounting principle, since the Fund had historically amortized such premiums to maturity for U.S. GAAP. Accordingly, the Fund has adopted ASU 2017-08 to amend the premium amortization period for certain purchased callable debt securities with non-contingent call features to the earliest call date. It is impracticable to evaluate the effect on individual prior periods, therefore the Fund applied the amendments on a modified retrospective basis by recognizing a cumulative effect adjustment that decreased the beginning of period cost of investments and increased the unrealized appreciation on investments of approximately $7,000.

This change in accounting policy has been made to comply with the newly issued accounting standard and had no impact on total accumulated earnings (loss) or the net asset value of

the Fund. With respect to the Fund's results of operations, amortization of premium to first call date accelerates amortization with the intent of more closely aligning the recognition of income on such bonds with the economics of the instrument.

In March 2020, FASB issued an Accounting Standard Update, ASU 2020-04, Reference Rate Reform (Topic 848) — Facilitation of the Effects of Reference Rate Reform on Financial Reporting ("ASU 2020-04"), which provides optional, temporary relief with respect to the financial reporting of contracts subject to certain types of modifications due to the planned discontinuation of the London Interbank Offered Rate ("LIBOR") and other IBOR-based reference rates at the end of 2021. The temporary relief provided by ASU 2020-04 is effective for certain reference rate-related contract modifications that occur during the period from March 12, 2020 through December 31, 2022. Management is evaluating the impact of ASU 2020-04 on the Fund's investments, derivatives, debt and other contracts that will undergo reference rate-related modifications as a result of the reference rate reform.

1.  Security Valuation: (1) Certain portfolio securities may be valued by an outside pricing service/vendor approved by the Trust's Board of Trustees (the "Trustees"). The pricing service/vendor may employ a pricing model that takes into account, among other things, bids, yield spreads and/or other market data and specific security characteristics. Alternatively, if a valuation is not available from an outside pricing service/vendor, and the security trades on an exchange, the security may be valued at its latest reported sale price (or at the exchange official closing price if such exchange reports an official closing price), prior to the time when assets are valued. If there are no sales on a given day and if there is no official exchange closing price for that day, the security is valued at the mean between the last reported bid and asked prices if such bid and asked prices are available in the relevant exchanges. If only bid prices are available then the latest bid price may be used. If Morgan Stanley Investment Management Inc. (the "Adviser") or Morgan Stanley Investment Management Limited ("MSIM Limited") (the "Sub-Adviser"), (effective October 1, 2019, MSIM Limited is no longer a Sub-Adviser to the Fund, a wholly-owned subsidiary of Morgan Stanley), determines that the price provided by the outside pricing service/vendor or exchange does not reflect the security's fair value or is unable to provide a price, prices from brokers or dealers may also be utilized. In these circumstances, the value of the security will be the mean of bid and asked prices obtained from brokers or dealers;

22

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

(2) futures are valued at the settlement price on the exchange on which they trade or, if a settlement price is unavailable, at the last sale price on the exchange; (3) over-the-counter ("OTC") swaps may be valued by an outside pricing service approved by the Trustees or quotes from a broker or dealer. Swaps cleared on a clearinghouse or exchange may be valued using the closing price provided by the clearinghouse or exchange; (4) when market quotations are not readily available, including circumstances under which the Adviser or the Sub-Adviser determines that the closing price, last sale price or the mean between the last reported bid and asked prices are not reflective of a security's market value, portfolio securities are valued at their fair value as determined in good faith under procedures established by and under the general supervision of the Trustees. Occasionally, developments affecting the closing prices of securities and other assets may occur between the times at which valuations of such securities are determined (that is, close of the foreign market on which the securities trade) and the close of business of the New York Stock Exchange ("NYSE"). If developments occur during such periods that are expected to materially affect the value of such securities, such valuations may be adjusted to reflect the estimated fair value of such securities as of the close of the NYSE, as determined in good faith by the Trustees or by the Adviser using a pricing service and/or procedures approved by the Trustees; (5) quotations of foreign portfolio securities, other assets and liabilities and forward contracts stated in foreign currency are translated into U.S. dollar equivalents at the prevailing market rates prior to the close of the NYSE; and (6) investments in mutual funds, including the Morgan Stanley Institutional Liquidity Funds, are valued at the net asset value ("NAV") as of the close of each business day.

The Trustees have responsibility for determining in good faith the fair value of the investments, and the Trustees may appoint others, such as the Trust's Adviser or a valuation committee, to assist the Trustees in determining fair value and to make the actual calculations pursuant to the fair valuation methodologies previously approved by the Trustees. Under procedures approved by the Trustees, the Trust's Adviser has formed a Valuation Committee whose members are approved by the Trustees. The Valuation Committee provides administration and oversight of the Trust's valuation policies and procedures, which are reviewed at least annually by

the Trustees. These procedures allow the Trust to utilize independent pricing services, quotations from securities and financial instrument dealers and other market sources to determine fair value.

2.  Fair Value Measurement: FASB Accounting Standards Codification^TM ("ASC") 820, "Fair Value Measurement" ("ASC 820"), defines fair value as the value that the Fund would receive to sell an investment or pay to transfer a liability in a timely transaction with an independent buyer in the principal market, or in the absence of a principal market, the most advantageous market for the investment or liability. ASC 820 establishes a three-tier hierarchy to distinguish between (1) inputs that reflect the assumptions market participants would use in valuing an asset or liability developed based on market data obtained from sources independent of the reporting entity (observable inputs) and (2) inputs that reflect the reporting entity's own assumptions about the assumptions market participants would use in valuing an asset or liability developed based on the best information available in the circumstances (unobservable inputs) and to establish classification of fair value measurements for disclosure purposes. Various inputs are used in determining the value of the Fund's investments. The inputs are summarized in the three broad levels listed below:

•  Level 1 – unadjusted quoted prices in active markets for identical investments

•  Level 2 – other significant observable inputs (including quoted prices for similar investments, interest rates, prepayment speeds, credit risk, etc.)

•  Level 3 – significant unobservable inputs including the Fund's own assumptions in determining the fair value of investments. Factors considered in making this determination may include, but are not limited to, information obtained by contacting the issuer, analysts, or the appropriate stock exchange (for exchange-traded securities), analysis of the issuer's financial statements or other available documents and, if necessary, available information concerning other securities in similar circumstances.

The inputs or methodology used for valuing securities are not necessarily an indication of the risk associated

23

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

with investing in those securities and the determination of the significance of a particular input to the fair value measurement in its entirety requires judgment and considers factors specific to each security.

The following is a summary of the inputs used to value the Fund's investments as of September 30, 2020:

Investment Type	Level 1 Unadjusted quoted prices (000)			Level 2 Other significant observable inputs (000)			Level 3 Significant unobservable inputs (000)		Total (000)
Assets:
Fixed Income Securities
Asset-Backed Securities	$	—		$	8,242		$	—	$	8,242
Collateralized Mortgage Obligations — Agency Collateral Series		—			7			—		7
Commercial Mortgage-Backed Securities		—			1,254			—		1,254
Corporate Bonds		—			11,276			—		11,276
Mortgages — Other		—			3,447			—		3,447
Sovereign		—			1,132			—		1,132
Total Fixed Income Securities		—			25,358			—		25,358
Short-Term Investments
Investment Company		118			—			—		118
U.S. Treasury Security		—			255			—		255
Total Short-Term Investments		118			255			—		373
Foreign Currency Forward Exchange Contracts		—			56			—		56
Credit Default Swap Agreement		—			115			—		115
Total Assets		118			25,784			—		25,902
Liabilities:
Foreign Currency Forward Exchange Contract		—			(1	)		—		(1	)
Futures Contracts		(7	)		—			—		(7	)
Total Liabilities		(7	)		(1	)		—		(8	)
Total	$	111		$	25,783		$	—	$	25,894

Transfers between investment levels may occur as the markets fluctuate and/or the availability of data used in an investment's valuation changes.

3.  Foreign Currency Translation and Foreign Investments: The books and records of the Fund are maintained in U.S. dollars. Foreign currency amounts are translated into U.S. dollars as follows:

–  investments, other assets and liabilities at the prevailing rate of exchange on the valuation date;

–  investment transactions and investment income at the prevailing rates of exchange on the dates of such transactions.

Although the net assets of the Fund are presented at the foreign exchange rates and market values at the close of the period, the Fund does not isolate that portion of the results of operations arising as a result of changes in the foreign exchange rates from the fluctuations arising from changes in the market prices of securities held at period end. Similarly, the Fund does not isolate the effect of changes in foreign exchange rates from the fluctuations arising from changes in the market prices of securities sold during the period. Accordingly, realized and unrealized foreign currency gains (losses) on investments in securities are included in the reported net realized and unrealized gains (losses) on investment transactions and balances. However, pursuant to U.S. federal income tax regulations, gains and losses from certain foreign currency transactions and the foreign currency portion of gains and losses realized on sales and maturities of foreign denominated debt securities are treated as ordinary income for U.S. federal income tax purposes.

Net realized gains (losses) on foreign currency transactions represent net foreign exchange gains (losses) from currency gains (losses) realized between the trade and settlement dates on securities transactions, and the difference between the amount of investment income and foreign withholding taxes recorded on the Fund's books and the U.S. dollar equivalent amounts actually received or paid. The change in unrealized currency gains (losses) on foreign currency transactions for the period is reflected in the Statement of Operations.

Foreign security and currency transactions may involve certain considerations and risks not typically associated with those of U.S. dollar denominated transactions as a result of, among other factors, fluctuations of exchange rates in relation to the U.S. dollar, the possibility of lower levels of governmental supervision and regulation of foreign securities markets and the possibility of political or economic instability.

Governmental approval for foreign investments may be required in advance of making an investment under certain circumstances in some countries, and the extent of foreign investments in domestic companies may be

24

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

subject to limitation in other countries. Foreign ownership limitations also may be imposed by the charters of individual companies to prevent, among other concerns, violations of foreign investment limitations. As a result, an additional class of shares (identified as "Foreign" in the Portfolio of Investments) may be created and offered for investment. The "local" and "foreign shares" market values may differ. In the absence of trading of the foreign shares in such markets, the Fund values the foreign shares at the closing exchange price of the local shares.

4.  Derivatives: The Fund may, but is not required to, use derivative instruments for a variety of purposes, including hedging, risk management, portfolio management or to earn income. Derivatives are financial instruments whose value is based, in part, on the value of an underlying asset, interest rate, index or financial instrument. Prevailing interest rates and volatility levels, among other things, also affect the value of derivative instruments. A derivative instrument often has risks similar to its underlying asset and may have additional risks, including imperfect correlation between the value of the derivative and the underlying asset, risks of default by the counterparty to certain transactions, magnification of losses incurred due to changes in the market value of the securities, instruments, indices or interest rates to which the derivative instrument relates, risks that the transactions may not be liquid and risks arising from margin requirements. The use of derivatives involves risks that are different from, and possibly greater than, the risks associated with other portfolio investments. Derivatives may involve the use of highly specialized instruments that require investment techniques and risk analyses different from those associated with other portfolio investments. All of the Fund's holdings, including derivative instruments, are marked-to-market each day with the change in value reflected in unrealized appreciation (depreciation). Upon disposition, a realized gain or loss is recognized.

Certain derivative transactions may give rise to a form of leverage. Leverage magnifies the potential for gain and the risk of loss. Leverage associated with derivative transactions may cause the Fund to liquidate portfolio positions when it may not be advantageous to do so to satisfy its obligations or to meet earmarking or segregation requirements, pursuant to applicable Securities and Exchange Commission rules and regulations, or may cause the Fund to be more volatile than if the Fund had

not been leveraged. Although the Adviser and/or Sub-Adviser seek to use derivatives to further the Fund's investment objectives, there is no assurance that the use of derivatives will achieve this result.

Following is a description of the derivative instruments and techniques that the Fund used during the period and their associated risks:

Options: With respect to options, the Fund is subject to equity risk, interest rate risk and foreign currency exchange risk in the normal course of pursuing its investment objectives. If the Fund buys an option, it buys a legal contract giving it the right to buy or sell a specific amount of the underlying instrument or foreign currency, or futures contract on the underlying instrument or foreign currency, at an agreed-upon price during a period of time or on a specified date typically in exchange for a premium paid by the Fund. The Fund may purchase and/or sell put and call options. Purchasing call options tends to increase the Fund's exposure to the underlying (or similar) instrument. Purchasing put options tends to decrease the Fund's exposure to the underlying (or similar) instrument. When entering into purchased option contracts, the Fund bears the risk of interest or exchange rates or securities prices moving unexpectedly, in which case, the Fund may not achieve the anticipated benefits of the purchased option contracts; however the risk of loss is limited to the premium paid. Purchased options are reported as part of "Total Investments in Securities" in the Statement of Assets and Liabilities. Premium paid for purchasing options which expired are treated as realized losses. If the Fund sells an option, it sells to another party the right to buy from or sell to the Fund a specific amount of the underlying instrument or foreign currency, or futures contract on the underlying instrument or foreign currency, at an agreed-upon price during a period of time or on a specified date typically in exchange for a premium received by the Fund. The Fund may write call and put options on stock indexes, futures, securities or currencies it owns or in which it may invest. Writing put options tend to increase the Fund's exposure to the underlying instrument. Writing call options tend to decrease the Fund's exposure to the underlying instruments. When the Fund writes a call or put option, an amount equal to the premium received is recorded as a liability. Any liability recorded is subsequently adjusted to reflect the current

25

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

value of the options written. Premiums received from writing options which expire are treated as realized gains. Premiums received from writing options which are exercised or are closed are added to or offset against the proceeds or amount paid on the transaction to determine the net realized gain or loss. The Fund as a writer of an option has no control over whether the underlying future, security or currency may be sold (call) or purchased (put) and as a result bears the market risk of an unfavorable change in the price of the future, security or currency underlying the written option. When options are purchased OTC, the Fund bears the risk that the counterparty that wrote the option will be unable or unwilling to perform its obligations under the option contract. Options may also be illiquid and the Fund may have difficulty closing out its position. A decision as to whether, when and how to use options involves the exercise of skill and judgment and even a well-conceived option transaction may be unsuccessful because of market behavior or unexpected events. The prices of options can be highly volatile and the use of options can lower total returns.

As of September 30, 2020, the Fund did not have any outstanding options written.

Futures: A futures contract is a standardized, exchange-traded agreement to buy or sell a specific quantity of an underlying asset, reference rate or index at a specific price at a specific future time. The value of a futures contract tends to increase and decrease in tandem with the value of the underlying instrument. Depending on the terms of the particular contract, futures contracts are settled through either physical delivery of the underlying instrument on the settlement date or by payment of a cash settlement amount on the settlement date. During the period the futures contract is open, payments are received from or made to the broker based upon changes in the value of the contract (the variation margin). A decision as to whether, when and how to use futures contracts involves the exercise of skill and judgment and even a well-conceived futures transaction may be unsuccessful because of market behavior or unexpected events. In addition to the derivatives risks discussed above, the prices of futures contracts can be highly volatile, using futures contracts can lower total return and the potential loss from futures contracts can exceed the Fund's initial investment in such contracts. No assurance can be given

that a liquid market will exist for any particular futures contract at any particular time. There is also the risk of loss by the Fund of margin deposits in the event of bankruptcy of a broker with which the Fund has open positions in the futures contract.

Swaps: The Fund may enter into OTC swap contracts or cleared swap transactions. A swap contract is an agreement between two parties pursuant to which the parties exchange payments at specified dates on the basis of a specified notional amount, with the payments calculated by reference to specified securities, indices, reference rates, currencies or other instruments. Typically swap agreements provide that when the period payment dates for both parties are the same, the payments are made on a net basis (i.e., the two payment streams are netted out, with only the net amount paid by one party to the other). The Fund's obligations or rights under a swap contract entered into on a net basis will generally be equal only to the net amount to be paid or received under the agreement, based on the relative values of the positions held by each party. Cleared swap transactions may help reduce counterparty credit risk. In a cleared swap, the Fund's ultimate counterparty is a clearinghouse rather than a swap dealer, bank or other financial institution. OTC swap agreements are not entered into or traded on exchanges and often there is no central clearing or guaranty function for OTC swaps. These OTC swaps are often subject to credit risk or the risk of default or non-performance by the counterparty. Both OTC and cleared swaps could result in losses if interest rates, foreign currency exchange rates or other factors are not correctly anticipated by the Fund or if the reference index, security or investments do not perform as expected. During the period swap agreements are open, payments are received from or made to the clearinghouse or counterparty based upon changes in the value of the contract (variation margin). The Dodd-Frank Wall Street Reform and Consumer Protection Act and related regulatory developments require the clearing and exchange-trading of certain standardized swap transactions. Mandatory exchange-trading and clearing is occurring on a phased-in basis.

The Fund's use of swaps during the period included those based on the credit of an underlying security commonly referred to as "credit default swaps." The Fund may be either the buyer or seller in a credit default swap.

26

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

Where the Fund is the buyer of a credit default swap contract, it would typically be entitled to receive the par (or other agreed-upon) value of a referenced debt obligation from the counterparty to the contract only in the event of a default or similar event by the issuer of the debt obligation. If no default occurs, the Fund would have paid to the counterparty a periodic stream of payments over the term of the contract and received no benefit from the contract. When the Fund is the seller of a credit default swap contract, it typically receives the stream of payments but is obligated to pay an amount equal to the par (or other agreed-upon) value of a referenced debt obligation upon the default or similar event by the issuer of the referenced debt obligation. The use of credit default swaps could result in losses to the Fund if the Adviser fails to correctly evaluate the creditworthiness of the issuer of the referenced debt obligation.

If the Fund is a seller of protection and a credit event occurs, as defined under the terms of that particular swap agreement, the Fund will either (i) pay to the buyer of protection an amount equal to the notional amount of the swap agreement and take delivery of the referenced obligation, other deliverable obligations or underlying securities comprising the referenced index or (ii) pay a net settlement amount in the form of cash or securities equal to the notional amount of the swap agreement less the recovery value of the referenced obligation or underlying securities comprising the referenced index. If the Fund is a buyer of protection and a credit event occurs, as defined under the terms of that particular swap agreement, the Fund will either (i) receive from the seller of protection an amount equal to the notional amount of the swap agreement and deliver the referenced obligation, other deliverable obligations or underlying securities comprising the referenced index or (ii) receive a net settlement amount in the form of cash or securities equal to the notional amount of the swap agreement less the recovery value of the referenced obligation or underlying securities comprising the referenced index. Recovery values are estimated by market makers considering either industry standard recovery rates or entity specific factors and considerations until a credit event occurs. If a credit event has occurred, the recovery value is determined by a facilitated auction whereby a minimum number of allowable broker bids, together with a specified valuation method, are used to calculate the settlement value. The Fund's maximum

risk of loss from counterparty risk, either as the protection seller or as the protection buyer, is the fair value of the swap agreement.

The current credit rating of each individual issuer is listed in the table following the Portfolio of Investments and serves as an indicator of the current status of the payment/performance risk of the credit derivative. Alternatively, for credit default swaps on an index of credits, the quoted market prices and current values serve as an indicator of the current status of the payment/performance risk of the credit derivative. Generally, lower credit ratings and increasing market values, in absolute terms, represent a deterioration of the credit and a greater likelihood of an adverse credit event of the issuer.

When the Fund has an unrealized loss on a swap agreement, the Fund has instructed the custodian to pledge cash or liquid securities as collateral with a value approximately equal to the amount of the unrealized loss. Collateral pledges are monitored and subsequently adjusted if and when the swap valuations fluctuate. If applicable, cash collateral is included with "Due from (to) Broker" in the Statement of Assets and Liabilities.

Upfront payments paid or received by the Fund will be reflected as an asset or liability, respectively, in the Statement of Assets and Liabilities.

Foreign Currency Forward Exchange Contracts: In connection with its investments in foreign securities, the Fund also entered into contracts with banks, brokers or dealers to purchase or sell securities or foreign currencies at a future date. A foreign currency forward exchange contract ("currency contract") is a negotiated agreement between the contracting parties to exchange a specified amount of currency at a specified future time at a specified rate. The rate can be higher or lower than the spot rate between the currencies that are the subject of the contract. Currency contracts may be used to protect against uncertainty in the level of future foreign currency exchange rates or to gain or modify exposure to a particular currency. In addition, the Fund may use cross currency hedging or proxy hedging with respect to currencies in which the Fund has or expects to have portfolio or currency exposure. Cross currency hedges involve the sale of one currency against the positive exposure to a different currency and may be used for hedging purposes or to establish an active exposure to the exchange

27

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

rate between any two currencies. To the extent hedged by the use of currency contracts, the precise matching of the currency contract amounts and the value of the securities involved will not generally be possible because the future value of such securities in foreign currencies will change as a consequence of market movements in the value of those securities between the date on which the contract is entered into and the date it matures. Furthermore, such transactions may reduce or preclude the opportunity for gain if the value of the currency should move in the direction opposite to the position taken. There is additional risk to the extent that currency contracts create exposure to currencies in which the Fund's securities are not denominated. Unanticipated changes in currency prices may result in poorer overall performance for the Fund than if it had not entered into such contracts. The use of currency contracts involves the risk of loss from the insolvency or bankruptcy of the counterparty to the contract or the failure of the counterparty to make payments or otherwise comply with the terms of the contract. A currency contract is marked-to-market daily and the change in market value is recorded by the Fund as unrealized gain or loss. The Fund records realized gains (losses) when the currency contract is closed equal to the difference between the value of the currency contract at the time it was opened and the value at the time it was closed.

FASB ASC 815, "Derivatives and Hedging" ("ASC 815"), is intended to improve financial reporting about derivative instruments by requiring enhanced disclosures to enable investors to better understand how and why the Fund uses derivative instruments, how these derivative instruments are accounted for and their effects on the Fund's financial position and results of operations.

The following tables set forth the fair value of the Fund's derivative contracts by primary risk exposure as of September 30, 2020:

	Asset Derivatives Statement of Assets and Liabilities Location	Primary Risk Exposure	Value (000)
Foreign Currency Forward Exchange Contracts	Unrealized Appreciation on Foreign Currency Forward Exchange Contracts	Currency Risk	$	56
Swap Agreement	Variation Margin on Swap Agreement	Credit Risk		115	(a)
Total			$	171

	Liability Derivatives Statement of Assets and Liabilities Location	Primary Risk Exposure	Value (000)
Foreign Currency Forward Exchange Contract	Unrealized Depreciation on Foreign Currency Forward Exchange Contract	Currency Risk	$	(1	)
Futures Contracts	Variation Margin on
	Futures Contracts	Interest Rate Risk		(7	)(a)
Total			$	(8	)

(a) This amount represents the cumulative appreciation (depreciation) as reported in the Portfolio of Investments. The Statement of Assets and Liabilities only reflects the current day's net variation margin.

The following tables set forth by primary risk exposure the Fund's realized gains (losses) and change in unrealized appreciation (depreciation) by type of derivative contract for the year ended September 30, 2020 in accordance with ASC 815:

Realized Gain (Loss)
Primary Risk Exposure	Derivative Type	Value (000)
Currency Risk	Foreign Currency Forward Exchange Contracts	$	(141	)
Interest Rate Risk	Futures Contracts		(61	)
Credit Risk	Swap Agreements		(243	)
Interest Rate Risk	Swap Agreements		(14	)
Interest Rate Risk	Written Option		15
	Total	$	(444	)
Change in Unrealized Appreciation (Depreciation)
Primary Risk Exposure	Derivative Type	Value (000)
Currency Risk	Foreign Currency Forward Exchange Contracts	$	14
Interest Rate Risk	Futures Contracts		(12	)
Credit Risk	Swap Agreements		117
	Total	$	119

At September 30, 2020, the Fund's derivative assets and liabilities are as follows:

Gross Amounts of Assets and Liabilities Presented in the Statement of Assets and Liabilities
Derivatives(b)	Assets(c) (000)		Liabilities(c) (000)
Foreign Currency Forward Exchange Contracts	$	56	$	(1	)

(b) Excludes exchange-traded derivatives.

(c) Absent an event of default or early termination, OTC derivative assets and liabilities are presented gross and not offset in the Statement of Assets and Liabilities.

The Fund typically enters into International Swaps and Derivatives Association, Inc. Master Agreements ("ISDA Master Agreements") or similar master agreements (collectively, "Master Agreements") with its contract counterparties for certain OTC derivatives in order to, among other things, reduce its credit risk to counterparties. ISDA Master Agreements include provisions for general obligations, representations, collateral and events

28

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

of default or termination. Under an ISDA Master Agreement, the Fund typically may offset with the counterparty certain OTC derivative financial instruments' payables and/or receivables with collateral held and/or posted and create one single net payment (close-out netting) in the event of default, termination and/or potential deterioration in the credit quality of the counterparty. Various Master Agreements govern the terms of certain transactions with counterparties, including transactions such as swap, forward, repurchase and reverse repurchase agreements. These Master Agreements typically attempt to reduce the counterparty risk associated with such transactions by specifying credit protection mechanisms and providing standardization that improves legal certainty. Cross-termination provisions under Master Agreements typically provide that a default in connection with one transaction between the Fund and a counterparty gives the non-defaulting party the right to terminate any other transactions in place with the defaulting party to create one single net payment due to/due from the defaulting party and may be a feature in certain Master Agreements. In the event the Fund exercises its right to terminate a Master Agreement after a counterparty experiences a termination event as defined in the Master Agreement, the return of collateral with market value in excess of the Fund's net liability may be delayed or denied.

The following tables present derivative financial instruments that are subject to enforceable netting arrangements as of September 30, 2020:

Gross Amounts Not Offset in the Statement of Assets and Liabilities
Counterparty	Gross Asset Derivatives Presented in the Statement of Assets and Liabilities (000)			Financial Instrument (000)			Collateral Received (000)		Net Amount (not less than $0) (000)
Australia and New Zealand Banking Group	$	15		$	—		$	—	$	15
Barclays Bank PLC		—	@		—			—		—	@
Citibank NA		40			(1	)		—		39
JPMorgan Chase Bank NA		1			—			—		1
UBS AG		—	@		—			—		—	@
Total	$	56		$	(1	)	$	—	$	55

Gross Amounts Not Offset in the Statement of Assets and Liabilities
Counterparty	Gross Liability Derivatives Presented in the Statement of Assets and Liabilities (000)		Financial Instrument (000)			Collateral Pledged (000)		Net Amount (not less than $0) (000)
Citibank NA	$	1	$	(1	)	$	—	$	0

@ Amount is less than $500.

For the year ended September 30, 2020, the approximate average monthly amount outstanding for each derivative type is as follows:

Foreign Currency Forward Exchange Contracts:
Average monthly principal amount	$	5,084,000
Futures Contracts:
Average monthly notional value	$	1,723,000
Swap Agreements:
Average monthly notional amount	$	1,844,000
Written Options:
Average monthly notional amount	$	167,000

5.  Indemnifications: The Trust enters into contracts that contain a variety of indemnifications. The Trust's maximum exposure under these arrangements is unknown. However, the Trust has not had prior claims or losses pursuant to these contracts and expects the risk of loss to be remote.

6.  Dividends and Distributions to Shareholders: Dividends and distributions to shareholders are recorded on the ex-dividend date. Dividends from net investment income, if any, are declared and paid monthly. Net realized capital gains, if any, are distributed at least annually.

7.  Security Transactions, Income and Expenses: Security transactions are accounted for on the trade date (date the order to buy or sell is executed). Realized gains and losses on the sale of investment securities are determined on the specific identified cost method. Dividend income and other distributions are recorded on the ex-dividend date (except for certain foreign dividends which may be recorded as soon as the Fund is informed of such dividends) net of applicable withholding taxes. Interest income is recognized on the accrual basis except where collection is in doubt. Discounts are accreted and premiums are amortized over the life of the respective securities. Most expenses of the Trust can be directly attributed to a

29

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

particular Fund. Expenses which cannot be directly attributed are apportioned among the Funds based upon relative net assets or other appropriate methods. Income, expenses (other than class specific expenses — distribution and shareholder services, transfer agency and sub transfer agency fees) and realized and unrealized gains or losses are allocated to each class of shares based upon their relative net assets.

B. Advisory/Sub-Advisory Fees: The Adviser, a wholly-owned subsidiary of Morgan Stanley, provides the Fund with advisory services under the terms of an Investment Advisory Agreement, paid quarterly, at the annual rate based on the daily net assets as follows:

First $500 million			Over $500 million
	0.40	%		0.35	%

Effective October 1, 2019, the Adviser will provide the Fund with advisory services under the terms of an Investment Advisory Agreement, paid quarterly, at an annual rate of 0.32% of the average daily net assets of the Fund.

For the year ended September 30, 2020, the advisory fee rate (net of waivers/rebate) was equivalent to an annual effective rate of 0.00% of the Fund's average daily net assets.

The Adviser has agreed to reduce its advisory fee and/or reimburse the Fund so that total annual Fund operating expenses, excluding certain investment related expenses, taxes, interest and other extraordinary expenses (including litigation), will not exceed 1.00% for Class I shares, 1.35% for Class A shares, 2.10% for Class C shares and 0.95% for Class IS shares. Effective October 1, 2019, the Adviser has agreed to reduce its advisory fee and/or reimburse the Fund so that total annual Fund operating expenses will not exceed 0.60% for Class I shares, 0.95% for Class A shares, 1.70% for Class C shares and 0.57% for Class IS shares. The fee waivers and/or expense reimbursements will continue for at least one year from the date of the Fund's prospectus or until such time as the Trustees act to discontinue all or a portion of such waivers and/or reimbursements when they deem such action is appropriate. For the year ended September 30, 2020, approximately $81,000 of advisory fees were waived and approximately $279,000 of other expenses were reimbursed by the Adviser pursuant to this arrangement.

The Adviser has entered into a Sub-Advisory Agreement with the Sub-Adviser, a wholly-owned subsidiary of Morgan Stanley. The Sub-Adviser provides the Fund with advisory services subject to the overall supervision of the Adviser and the Fund's

Officers and Trustees. The Adviser pays the Sub-Adviser on a monthly basis a portion of the net advisory fees the Adviser receives from the Fund.

Effective October 1, 2019, MSIM Limited is no longer a Sub-Adviser to the Fund.

C. Administration Fees: The Adviser also serves as Administrator to the Trust and provides administrative services pursuant to an Administration Agreement for an annual fee, accrued daily and paid monthly, of 0.08% of the Fund's average daily net assets. Under a Sub-Administration Agreement between the Administrator and State Street Bank and Trust Company ("State Street"), State Street provides certain administrative services to the Trust. For such services, the Administrator pays State Street a portion of the fee the Administrator receives from the Fund.

D. Distribution and Shareholder Services Fees: Morgan Stanley Distribution, Inc. ("MSDI" or the "Distributor"), a wholly-owned subsidiary of the Adviser and an indirect subsidiary of Morgan Stanley, serves as the Trust's Distributor of Fund shares pursuant to a Distribution Agreement. The Trust has adopted a Shareholder Services Plan with respect to Class A shares pursuant to Rule 12b-1 under the Act. Under the Shareholder Services Plan, the Fund pays the Distributor a shareholder services fee, accrued daily and paid monthly, at an annual rate of 0.25% of the Fund's average daily net assets attributable to Class A shares.

The Trust has adopted a Distribution and Shareholder Services Plan with respect to Class C shares pursuant to Rule 12b-1 under the Act. Under the Distribution and Shareholder Services Plan, the Fund pays the Distributor a distribution fee, accrued daily and paid monthly, at an annual rate of 0.75% and a shareholder services fee, accrued daily and paid monthly, at an annual rate of 0.25% of the Fund's average daily net assets attributable to Class C shares.

The distribution and shareholder services fees are used to support the expenses associated with servicing and maintaining accounts. The Distributor may compensate other parties for providing shareholder support services to investors who purchase Class A and Class C shares.

E. Dividend Disbursing and Transfer Agent: The Trust's dividend disbursing and transfer agent is DST Asset Manager Solutions, Inc. ("DST"). Pursuant to a Transfer Agency Agreement, the Trust pays DST a fee based on the number of classes, accounts and transactions relating to the Funds of the Trust.

30

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

F. Custodian Fees: State Street (the "Custodian") also serves as Custodian for the Trust in accordance with a Custodian Agreement. The Custodian holds cash, securities and other assets of the Trust as required by the Act. Custody fees are payable monthly based on assets held in custody, investment purchases and sales activity and account maintenance fees, plus reimbursement for certain out-of-pocket expenses.

G. Security Transactions and Transactions with Affiliates: For the year ended September 30, 2020, purchases and sales of investment securities for the Fund, other than long-term U.S. Government securities and short-term investments were approximately $27,300,000 and $10,611,000, respectively. For the year ended September 30, 2020, purchases and sales of long-term U.S. Government securities were approximately $25,505,000 and $25,910,000, respectively.

The Fund invests in the Institutional Class of the Morgan Stanley Institutional Liquidity Funds — Government Portfolio (the "Liquidity Funds"), an open-end management investment company managed by the Adviser. Advisory fees paid by the Fund are reduced by an amount equal to its pro-rata share of the advisory and administration fees paid by the Fund due to its investment in the Liquidity Funds. For the year ended September 30, 2020, advisory fees paid were reduced by approximately $1,000 relating to the Fund's investment in the Liquidity Funds.

A summary of the Fund's transactions in shares of affiliated investments during the year ended September 30, 2020 is as follows:

Affiliated Investment Company	Value September 30, 2019 (000)		Purchases at Cost (000)		Proceeds from Sales (000)		Dividend Income (000)
Liquidity Funds	$	614	$	22,256	$	22,752	$	5

Affiliated Investment Company (cont'd)	Realized Gain (Loss) (000)		Change in Unrealized Appreciation (Depreciation) (000)		Value September 30, 2020 (000)
Liquidity Funds	$	—	$	—	$	118

The Fund is permitted to purchase and sell securities ("cross-trade") from and to other Morgan Stanley funds as well as other funds and client accounts for which the Adviser or an affiliate of the Adviser serves as investment adviser, pursuant to procedures approved by the Trustees in compliance with Rule 17a-7 under the Act (the "Rule"). Each cross-trade is executed at the current market price in compliance with provisions of the Rule. For the year ended September 30, 2020, the Fund did not engage in any cross-trade transactions.

The Fund has an unfunded Deferred Compensation Plan (the "Compensation Plan"), which allows each independent Trustee to defer payment of all, or a portion, of the fees he or she receives for serving on the Board of Trustees. Each eligible Trustee generally may elect to have the deferred amounts credited with a return equal to the total return on one or more of the Morgan Stanley funds that are offered as investment options under the Compensation Plan. Appreciation/depreciation and distributions received from these investments are recorded with an offsetting increase/decrease in the deferred compensation obligation and do not affect the NAV of the Fund.

H. Federal Income Taxes: It is the Fund's intention to continue to qualify as a regulated investment company and distribute all of its taxable and tax-exempt income. Accordingly, no provision for federal income taxes is required in the financial statements.

The Fund may be subject to taxes imposed by countries in which it invests. Such taxes are generally based on income and/or capital gains earned or repatriated. Taxes are accrued based on net investment income, net realized gains and net unrealized appreciation as such income and/or gains are earned. Taxes may also be based on transactions in foreign currency and are accrued based on the value of investments denominated in such currency.

FASB ASC 740-10, "Income Taxes — Overall", sets forth a minimum threshold for financial statement recognition of the benefit of a tax position taken or expected to be taken in a tax return. Management has concluded there are no significant uncertain tax positions that would require recognition in the financial statements. If applicable, the Fund recognizes interest accrued related to unrecognized tax benefits in "Interest Expense" and penalties in "Other Expenses" in the Statement of Operations. The Fund files tax returns with the U.S. Internal Revenue Service, New York and various states. Generally, each of the tax years in the four-year period ended September 30, 2020 remains subject to examination by taxing authorities.

The tax character of distributions paid may differ from the character of distributions shown for GAAP purposes due to short-term capital gains being treated as ordinary income for tax purposes. The tax character of distributions paid during fiscal years 2020 and 2019 was as follows:

2020 Distributions Paid From:				2019 Distributions Paid From:
Ordinary Income (000)		Long-Term Capital Gain (000)		Ordinary Income (000)		Long-Term Capital Gain (000)
$	755	$	—	$	457	$	146

31

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

The amount and character of income and gains to be distributed are determined in accordance with income tax regulations which may differ from GAAP. These book/tax differences are either considered temporary or permanent in nature.

Temporary differences are attributable to differing book and tax treatments for the timing of the recognition of gains (losses) on certain investment transactions and the timing of the deductibility of certain expenses.

Permanent differences, due to tax adjustments on debt securities, resulted in the following reclassifications among the components of net assets at September 30, 2020:

Total Accumulated Loss (000)			Paid-in- Capital (000)
$	(2	)	$	2

At September 30, 2020, the components of distributable earnings for the Fund on a tax basis were as follows:

Undistributed Ordinary Income (000)		Undistributed Long-Term Capital Gain (000)
$	184	$	—

At September 30, 2020, the Fund had available for federal income tax purposes unused short-term and long-term capital losses of approximately $396,000 and $72,000, respectively, that do not have an expiration date.

To the extent that capital loss carryforwards are used to offset any future capital gains realized, no capital gains tax liability will be incurred by the Fund for gains realized and not distributed. To the extent that capital gains are offset, such gains will not be distributed to the shareholders.

I. Credit Facility: The Trust and other Morgan Stanley funds participated in a $300,000,000 committed, unsecured revolving line of credit facility (the "Facility") with State Street. This Facility is to be used for temporary emergency purposes or funding of shareholder redemption requests. The interest rate on borrowings is based on the federal funds rate or 1 month LIBOR rate plus a spread. The Facility also has a commitment fee of 0.25% per annum based on the unused portion of the Facility. During the year ended September 30, 2020, the Fund did not have any borrowings under the Facility.

J. Other: At September 30, 2020, the Fund did not have record owners of 10% or greater.

K. Market Risk: Certain impacts to public health conditions particular to the coronavirus (COVID-19) outbreak could

impact the operations and financial performance of certain of the Fund's investments. The extent of the impact to the financial performance of the Fund's investments will depend on future developments, including (i) the duration and spread of the outbreak, (ii) the restrictions and advisories, (iii) the effects on the financial markets, and (iv) the effects on the economy overall, all of which are highly uncertain and cannot be predicted. If the financial performance of the Fund's investments is impacted because of these factors for an extended period, the Fund's investment results may be adversely affected.

L. LIBOR Risk: The Fund's investments, payment obligations and financing terms may be based on floating rates, such as London Interbank Offer Rate ("LIBOR"), Euro Interbank Offered Rate and other similar types of reference rates (each, a "Reference Rate"). These Reference Rates are generally intended to represent the rate at which contributing banks may obtain short-term borrowings from each other within certain financial markets. On July 27, 2017, the Chief Executive of the UK Financial Conduct Authority ("FCA"), which regulates LIBOR, announced that the FCA will no longer persuade nor require banks to submit rates for the calculation of LIBOR and certain other Reference Rates after 2021. Such announcement indicates that the continuation of LIBOR and other Reference Rates on the current basis cannot and will not be guaranteed after the end of 2021. This announcement and any additional regulatory or market changes may have an adverse impact on the Fund or its investments.

In advance of 2022, regulators and market participants are currently engaged in identifying successor Reference Rates ("Alternative Reference Rates"). Additionally, prior to the end of 2021, it is expected that market participants will focus on the transition mechanisms by which the Reference Rates in existing contracts or instruments may be amended, whether through marketwide protocols, fallback contractual provisions, bespoke negotiations or amendments or otherwise. Nonetheless, the termination of certain Reference Rates presents risks to the Fund. At this time, it is not possible to completely identify or predict the effect of any such changes, any establishment of Alternative Reference Rates or any other reforms to Reference Rates that may be enacted in the UK or elsewhere. The elimination of a Reference Rate or any other changes or reforms to the determination or supervision of Reference Rates could have an adverse impact on the market for or value of any securities or payments linked to those Reference Rates and other financial obligations held by the Fund or on its overall financial condition or results of operations.

32

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Report of Independent Registered Public Accounting Firm

To the Shareholders and Board of Trustees of
Morgan Stanley Institutional Fund Trust —
Strategic Income Portfolio

Opinion on the Financial Statements

We have audited the accompanying statement of assets and liabilities of Strategic Income Portfolio (the "Fund") (one of the funds constituting Morgan Stanley Institutional Fund Trust (the "Trust")), including the portfolio of investments, as of September 30, 2020, and the related statement of operations for the year then ended, the statements of changes in net assets for each of the two years in the period then ended, the financial highlights for each of the five years in the period then ended and the related notes (collectively referred to as the "financial statements"). In our opinion, the financial statements present fairly, in all material respects, the financial position of Strategic Income Portfolio (one of the funds constituting Morgan Stanley Institutional Fund Trust) at September 30, 2020, the results of its operations for the year then ended, the changes in its net assets for each of the two years in the period then ended and its financial highlights for each of the five years in the period then ended, in conformity with U.S. generally accepted accounting principles.

Basis for Opinion

These financial statements are the responsibility of the Trust's management. Our responsibility is to express an opinion on the Fund's financial statements based on our audits. We are a public accounting firm registered with the Public Company Accounting Oversight Board (United States) ("PCAOB") and are required to be independent with respect to the Trust in accordance with the U.S. federal securities law and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB.

We conducted our audits in accordance with the standards of the PCAOB. Those standards require that we plan and perform the audit to obtain reasonable assurance about whether the financial statements are free of material misstatement, whether due to error or fraud. The Trust is not required to have, nor were we engaged to perform, an audit of the Trust's internal control over financial reporting. As part of our audits we are required to obtain an understanding of internal control over financial reporting but not for the purpose of expressing an opinion on the effectiveness of the Trust's internal control over financial reporting. Accordingly, we express no such opinion.

Our audits included performing procedures to assess the risks of material misstatement of the financial statements, whether due to error or fraud, and performing procedures that respond to those risks. Such procedures included examining, on a test basis, evidence regarding the amounts and disclosures in the financial statements. Our procedures included confirmation of securities owned as of September 30, 2020 by correspondence with the custodian and brokers or by other appropriate auditing procedures where replies from brokers were not received. Our audits also included evaluating the accounting principles used and significant estimates made by management, as well as evaluating the overall presentation of the financial statements. We believe that our audits provide a reasonable basis for our opinion.

We have served as the auditor of one or more Morgan Stanley investment companies since 2000.
Boston, Massachusetts
November 24, 2020

33

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Advisory Agreement Approval (unaudited)

Nature, Extent and Quality of Services

The Board reviewed and considered the nature and extent of the investment advisory services provided by the Adviser under the advisory agreement, including portfolio management, investment research and equity and fixed income securities trading. The Board also reviewed and considered the nature and extent of the non-advisory, administrative services provided by the Administrator under the administration agreement, including accounting, operations, clerical, bookkeeping, compliance, business management and planning, legal services and the provision of supplies, office space and utilities at the Adviser's expense. The Board also considered the Adviser's investment in personnel and infrastructure that benefits the Fund. (The Adviser and Administrator together are referred to as the "Adviser" and the advisory and administration agreements together are referred to as the "Management Agreement.") The Board also considered that the Adviser serves a variety of other investment advisory clients and has experience overseeing service providers. The Board also compared the nature of the services provided by the Adviser with similar services provided by non-affiliated advisers as prepared by Broadridge Financial Solutions, Inc. ("Broadridge").

The Board reviewed and considered the qualifications of the portfolio managers, the senior administrative managers and other key personnel of the Adviser who provide the advisory and administrative services to the Fund. The Board determined that the Adviser's portfolio managers and key personnel are well qualified by education and/or training and experience to perform the services in an efficient and professional manner. The Board concluded that the nature and extent of the advisory and administrative services provided were necessary and appropriate for the conduct of the business and investment activities of the Fund and supported its decision to approve the Management Agreement.

Performance, Fees and Expenses of the Fund

The Board reviewed the performance, fees and expenses of the Fund compared to its peers, as prepared by Broadridge, and to appropriate benchmarks where applicable. The Board discussed with the Adviser the performance goals and the actual results achieved in managing the Fund. When considering a fund's performance, the Board and the Adviser place emphasis on trends and longer-term returns (focusing on one-year, three-year and five-year performance, as of December 31, 2019, or since inception, as applicable). When a fund underperforms its benchmark and/or its peer group average, the Board and the Adviser discuss the causes of such underperformance and, where necessary, they discuss specific changes to investment strategy or investment personnel. The Board noted that the Fund's performance was better than its peer group average for three- and five-year periods but below its peer group average for the one-year period. The Board discussed with the Adviser the level of the advisory and administration fees (together, the "management fee") for this Fund relative to comparable funds and/or other accounts advised by the Adviser and/or compared to its peers as prepared by Broadridge. In addition to the management fee, the Board also reviewed the Fund's total expense ratio. When a fund's management fee and/or its total expense ratio are higher than its peers, the Board and the Adviser discuss the reasons for this and, where appropriate, they discuss possible waivers and/or caps. The Board noted that the Fund's management fee was lower than its peer group average and the total expense ratio was higher than its peer group average. After discussion, the Board concluded that the Fund's (i) performance and management fee were competitive with its peer group averages and (ii) total expense ratio was acceptable.

Economies of Scale

The Board considered the size and growth prospects of the Fund and how that relates to the Fund's total expense ratio and particularly the Fund's management fee rate, which includes a breakpoint. In conjunction with its review of the Adviser's profitability, the Board discussed with the Adviser how a change in assets can affect the efficiency or effectiveness of managing the Fund and whether the management fee level is appropriate relative to current and projected asset levels and/or whether the management fee structure reflects economies of scale as asset levels change. The Board has determined that its review of the actual and/or potential economies of scale of the Fund supports its decision to approve the Management Agreement.

Profitability of the Adviser and Affiliates

The Board considered information concerning the costs incurred and profits realized by the Adviser and its affiliates during the last year from their relationship with the Fund and during the last two years from their relationship with the Morgan Stanley Fund Complex and reviewed with the Adviser the cost allocation methodology used to determine the profitability of the Adviser and affiliates. The Board has determined that its review of the analysis of the Adviser's expenses and profitability supports its decision to approve the Management Agreement.

34

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Advisory Agreement Approval (unaudited) (cont'd)

Other Benefits of the Relationship

The Board considered other direct and indirect benefits to the Adviser and/or its affiliates derived from their relationship with the Fund and other funds advised by the Adviser. These benefits may include, among other things, fees for trading, distribution and/or shareholder servicing and for transaction processing and reporting platforms used by securities lending agents, and research received by the Adviser generated from commission dollars spent on funds' portfolio trading. The Board reviewed with the Adviser these arrangements and the reasonableness of the Adviser's costs relative to the services performed. The Board has determined that its review of the other benefits received by the Adviser or its affiliates supports its decision to approve the Management Agreement.

Resources of the Adviser and Historical Relationship Between the Fund and the Adviser

The Board considered whether the Adviser is financially sound and has the resources necessary to perform its obligations under the Management Agreement. The Board also reviewed and considered the historical relationship between the Fund and the Adviser, including the organizational structure of the Adviser, the policies and procedures formulated and adopted by the Adviser for managing the Fund's operations and the Board's confidence in the competence and integrity of the senior managers and key personnel of the Adviser. The Board concluded that the Adviser has the financial resources necessary to fulfill its obligations under the Management Agreement and that it is beneficial for the Fund to continue its relationship with the Adviser.

Other Factors and Current Trends

The Board considered the controls and procedures adopted and implemented by the Adviser and monitored by the Fund's Chief Compliance Officer and concluded that the conduct of business by the Adviser indicates a good faith effort on its part to adhere to high ethical standards in the conduct of the Fund's business.

As part of the Board's review, the Board received information from management on the impact of COVID-19 on the firm generally and the Adviser and the Fund in particular including, among other information, the pandemic's current and expected impact on the Fund's performance and operations.

General Conclusion

After considering and weighing all of the above factors, with various written materials and verbal information presented by the Adviser, the Board concluded that it would be in the best interest of the Fund and its shareholders to approve renewal of the Management Agreement for another year. In reaching this conclusion the Board did not give particular weight to any single piece of information or factor referenced above. The Board considered these factors and information over the course of the year and in numerous meetings, some of which were in executive session with only the independent Board members and their counsel present. It is possible that individual Board members may have weighed these factors, and the information presented, differently in reaching their individual decisions to approve the Management Agreement.

35

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Liquidity Risk Management Program (unaudited)

In compliance with Rule 22e-4 under the Investment Company Act of 1940, as amended (the "Liquidity Rule"), the Fund has adopted and implemented a liquidity risk management program (the "Program"), which is reasonably designed to assess and manage the risk that the Fund could not meet requests to redeem shares issued by the Fund without significant dilution of remaining investors' interests in the Fund (i.e., liquidity risk). The Fund's Board of Trustees (the "Board") previously approved the designation of the Liquidity Risk Subcommittee (the "LRS") as Program administrator. The LRS is comprised of representatives from various divisions within Morgan Stanley Investment Management.

At a meeting held on April 22-23, 2020, the Board reviewed a written report prepared by the LRS that addressed the Program's operation and assessed its adequacy, and effectiveness of implementation for the period from December 1, 2018, through December 31, 2019, as required under the Liquidity Rule. The report concluded that the Program operated effectively and was adequately and effectively implemented in all material aspects, and that the relevant controls and safeguards were appropriately designed to enable the LRS to administer the Program in compliance with the Liquidity Rule.

In accordance with the Program, the LRS assessed each Fund's liquidity risk no less frequently than annually taking into consideration certain factors, as applicable, such as (i) investment strategy and liquidity of portfolio investments, (ii) short-term and long-term cash flow projections and (iii) holdings of cash and cash equivalents and borrowing arrangements and other funding sources. Certain factors are considered under both normal and reasonably foreseeable stressed conditions.

Each Fund portfolio investment is classified into one of four liquidity categories, which classification is assessed at least monthly by the LRS. The classification is based on a determination of the number of days it is reasonably expected to take to convert the investment into cash, or sell or dispose of the investment, in current market conditions without significantly changing the market value of the investment. Liquidity classification determinations take into account various market, trading and investment-specific considerations, as well as market depth, and in some cases utilize third-party vendor data.

The Liquidity Rule limits a fund's investments in illiquid investments to 15% of its net assets and requires funds that do not primarily hold assets that are highly liquid investments to determine and maintain a minimum percentage of the fund's net assets to be invested in highly liquid investments (highly liquid investment minimum or "HLIM"). The LRS believes that the Program includes provisions reasonably designed to review, monitor and comply with the 15% limit on illiquid investments and for determining, periodically reviewing and complying with the HLIM requirement, as applicable.

There can be no assurance that the Program will achieve its objectives under all circumstances in the future. Please refer to the Fund's prospectus for more information regarding the Fund's exposure to liquidity risk and other risks to which it may be subject.

36

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Privacy Notice (unaudited)  April 2019

FACTS	WHAT DOES MSIM DO WITH YOUR PERSONAL INFORMATION?
Why?	Financial companies choose how they share your personal information. Federal law gives consumers the right to limit some but not all sharing. Federal law also requires us to tell you how we collect, share, and protect your personal information. Please read this notice carefully to understand what we do.
What?	The types of personal information we collect and share depend on the product or service you have with us. This information can include: n Social Security number and income n investment experience and risk tolerance n checking account number and wire transfer instructions
How?	All financial companies need to share customers' personal information to run their everyday business. In the section below, we list the reasons financial companies can share their customers' personal information; the reasons MSIM chooses to share; and whether you can limit this sharing.

Reasons we can share your personal information	Does MSIM share?	Can you limit this sharing?
For our everyday business purposes — such as to process your transactions, maintain your account(s), respond to court orders and legal investigations, or report to credit bureaus	Yes	No
For our marketing purposes — to offer our products and services to you	Yes	No
For joint marketing with other financial companies	No	We don't share
For our affiliates' everyday business purposes — information about your transactions and experiences	Yes	No
For our affiliates' everyday business purposes — information about your creditworthiness	No	We don't share
For our affiliates to market to you	No	We don't share
For non-affiliates to market to you	No	We don't share

Questions?Call toll-free (844) 312-6327 or email: imprivacyinquiries@morganstanley.com

37

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Privacy Notice (unaudited) (cont'd)  April 2019

Who we are

Who is providing this notice? Morgan Stanley Investment Management, Inc. and its affiliated registered investment advisers, registered broker-dealers, and registered and unregistered funds ("MSIM")

What we do

How does MSIM protect my personal information?	To protect your personal information from unauthorized access and use, we use security measures that comply with federal law. These measures include computer safeguards and secured files and buildings. We have policies governing the proper handling of customer information by personnel and requiring third parties that provide support to adhere to appropriate security standards with respect to such information.
How does MSIM collect my personal information?	We collect your personal information, for example, when you n open an account or make deposits or withdrawals from your account n buy securities from us or make a wire transfer n give us your contact information We also collect your personal information from others, such as credit bureaus, affiliates, or other companies.
Why can't I limit all sharing?	Federal law gives you the right to limit only n sharing for affiliates' everyday business purposes — information about your creditworthiness n affiliates from using your information to market to you n sharing for non-affiliates to market to you State laws and individual companies may give you additional rights to limit sharing. See below for more on your rights under state law.

Definitions

Affiliates	Companies related by common ownership or control. They can be financial and non-financial companies. n Our affiliates include companies with a Morgan Stanley name and financial companies such as Morgan Stanley Smith Barney LLC and Morgan Stanley & Co.
Non-affiliates	Companies not related by common ownership or control. They can be financial and non-financial companies. n MSIM does not share with non-affiliates so they can market to you.
Joint marketing	A formal agreement between non-affiliated financial companies that together market financial products or services to you. n MSIM doesn't jointly market

Other important information

Vermont: Except as permitted by law, we will not share personal information we collect about Vermont residents with Non-affiliates unless you provide us with your written consent to share such information.

California: Except as permitted by law, we will not share personal information we collect about California residents with Non-affiliates and we will limit sharing such personal information with our Affiliates to comply with California privacy laws that apply to us.

38

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited)

Independent Trustees:

Name, Address and Birth Year of Independent Trustee	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years and Other Relevant Professional Experience	Number of Funds in Fund Complex Overseen by Independent Trustee**		Other Directorships Held by Independent Trustee***
Frank L. Bowman c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1944	Trustee	Since August 2006	President, Strategic Decisions, LLC (consulting) (since February 2009); Director or Trustee of various Morgan Stanley Funds (since August 2006); Chairperson of the Compliance and Insurance Committee (since October 2015); formerly, Chairperson of the Insurance Sub-Committee of the Compliance and Insurance Committee (2007-2015); served as President and Chief Executive Officer of the Nuclear Energy Institute (policy organization) (February 2005-November 2008); retired as Admiral, U.S. Navy after serving over 38 years on active duty including 8 years as Director of the Naval Nuclear Propulsion Program in the Department of the Navy and the U.S. Department of Energy (1996-2004); served as Chief of Naval Personnel (July 1994-September 1996) and on the Joint Staff as Director of Political Military Affairs (June 1992-July 1994); knighted as Honorary Knight Commander of the Most Excellent Order of the British Empire; awarded the Officier de l'Orde National du Mérite by the French Government; elected to the National Academy of Engineering (2009).		86	Director of Naval and Nuclear Technologies LLP; Director Emeritus of the Armed Services YMCA; Member of the National Security Advisory Council of the Center for U.S. Global Engagement and a member of the CNA Military Advisory Board; Trustee of Fairhaven United Methodist Church; Member of the Board of Advisors of the Dolphin Scholarship Foundation; Director of other various non-profit organizations; Formerly, Director of BP p.l.c. (November 2010-May 2019).
Kathleen A. Dennis c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1953	Trustee	Since August 2006	President, Cedarwood Associates (mutual fund and investment management consulting) (since July 2006); Chairperson of the Liquidity and Alternatives Sub-Committee of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 2006); formerly, Senior Managing Director of Victory Capital Management (1993-2006).		86	Director of various non-profit organizations.
Nancy C. Everett c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1955	Trustee	Since January 2015	Chief Executive Officer, Virginia Commonwealth University Investment Company (since November 2015); Owner, OBIR, LLC (institutional investment management consulting) (since June 2014); formerly, Managing Director, BlackRock, Inc. (February 2011-December 2013); and Chief Executive Officer, General Motors Asset Management (a/k/a Promark Global Advisors, Inc.) (June 2005-May 2010).		87	Formerly, Member of Virginia Commonwealth University School of Business Foundation (2005-2016); Member of Virginia Commonwealth University Board of Visitors (2013-2015); Member of Committee on Directors for Emerging Markets Growth Fund, Inc. (2007-2010); Chairperson of Performance Equity Management, LLC (2006-2010); and Chairperson, GMAM Absolute Return Strategies Fund, LLC (2006-2010).

39

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Address and Birth Year of Independent Trustee	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years and Other Relevant Professional Experience	Number of Funds in Fund Complex Overseen by Independent Trustee**		Other Directorships Held by Independent Trustee***
Jakki L. Haussler c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1957	Trustee	Since January 2015	Chairman, Opus Capital Group (since January 1996); formerly, Chief Executive Officer, Opus Capital Group (1996-2019); Director, Capvest Venture Fund, LP (May 2000-December 2011); Partner, Adena Ventures, LP (July 1999-December 2010); Director, The Victory Funds (February 2005-July 2008).		87	Director of Service Corporation International and Member, Audit Committee and Investment Committee; Director of Cincinnati Bell Inc. and Member, Audit Committee and Governance and Nominating Committee; Director of Northern Kentucky University Foundation and Member, Investment Committee; Member of Chase College of Law Transactional Law Practice Center Board of Advisors; Director of Chase College of Law Board of Visitors; formerly, Member, University of Cincinnati Foundation Investment Committee; Member, Miami University Board of Visitors (2008-2011); Trustee of Victory Funds (2005-2008) and Chairman, Investment Committee (2007-2008); Member, Service Provider Committee (2005-2008) and Director of Best Transport (2006-2019).
Dr. Manuel H. Johnson c/o Johnson Smick International, Inc. 220 I Street, NE — Suite 200 Washington, D.C. 20002 Birth Year 1949	Trustee	Since July 1991	Senior Partner, Johnson Smick International, Inc. (consulting firm); Chairperson of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since July 1991); Co-Chairman and a founder of the Group of Seven Council (G7C) (international economic commission); formerly, Chairperson of the Audit Committee (July 1991-September 2006), Vice Chairman of the Board of Governors of the Federal Reserve System and Assistant Secretary of the U.S. Treasury.		86	Director of NVR, Inc. (home construction).
Joseph J. Kearns c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1942	Trustee	Since August 1994	Senior Adviser, Kearns & Associates LLC (investment consulting); Chairperson of the Audit Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 1994); Director, Rubicorn Investments (since February 2019); formerly, Deputy Chairperson of the Audit Committee (July 2003-September 2006) and Chairperson of the Audit Committee of various Morgan Stanley Funds (since August 1994); CFO of the J. Paul Getty Trust (1982-1999).		87	Prior to August 10, 2016, Director of Electro Rent Corporation (equipment leasing); Prior to December 31, 2013, Director of The Ford Family Foundation.

40

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Address and Birth Year of Independent Trustee	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years and Other Relevant Professional Experience	Number of Funds in Fund Complex Overseen by Independent Trustee**		Other Directorships Held by Independent Trustee***
Michael F. Klein c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1958	Trustee	Since August 2006	Managing Director, Aetos Alternatives Management, LP (since March 2000); Co-President, Aetos Alternatives Management, LP (since January 2004) and Co-Chief Executive Officer of Aetos Alternatives Management, LP (since August 2013); Chairperson of the Fixed Income Sub-Committee of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 2006); formerly, Managing Director, Morgan Stanley & Co. Inc. and Morgan Stanley Dean Witter Investment Management and President, various Morgan Stanley Funds (June 1998-March 2000); Principal, Morgan Stanley & Co. Inc. and Morgan Stanley Dean Witter Investment Management (August 1997-December 1999).		86	Director of certain investment funds managed or sponsored by Aetos Alternatives Management, LP; Director of Sanitized AG and Sanitized Marketing AG (specialty chemicals).
Patricia Maleski c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1960	Trustee	Since January 2017	Managing Director, JPMorgan Asset Management (2004-2016); Oversight and Control Head of Fiduciary and Conflicts of Interest Program (2015-2016); Chief Control Officer-Global Asset Management (2013-2015); President, JPMorgan Funds (2010-2013); Chief Administrative Officer (2004-2013); various other positions including Treasurer and Board Liaison (since 2001).		87	None.
W. Allen Reed c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1947	Chair of the Board and Trustee	Chair of the Boards since August 2020 and Trustee since August 2006	Chair of the Boards of various Morgan Stanley Funds (since August 2020); Chairperson of the Governance Committee; Chairperson of the Equity Sub-Committee of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 2006); formerly, Vice Chair of the Boards of various Morgan Stanley Funds (January 2020-August 2020); President and Chief Executive Officer of General Motors Asset Management; Chairman and Chief Executive Officer of the GM Trust Bank and Corporate Vice President of General Motors Corporation (August 1994-December 2005).		86	Formerly, Director of Legg Mason, Inc. (2006-2019); and Director of the Auburn University Foundation (2010-2015).

*  This is the earliest date the Trustee began serving the Morgan Stanley Funds. Each Trustee serves an indefinite term, until his or her successor is elected.

**  The Fund Complex includes (as of December 31, 2019) all open-end and closed-end funds (including all of their portfolios) advised by Morgan Stanley Investment Management Inc. (the "Adviser") and any funds that have an adviser that is an affiliated person of the Adviser (including, but not limited to, Morgan Stanley AIP GP LP).

***  This includes any directorships at public companies and registered investment companies held by the Trustee at any time during the past five years.

41

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited) (cont'd)

Executive Officers:

Name, Address and Birth Year of Executive Officer	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years
John H. Gernon 522 Fifth Avenue New York, NY 10036 Birth Year 1963	President and Principal Executive Officer	Since September 2013	President and Principal Executive Officer of the Equity and Fixed Income Funds and the Morgan Stanley AIP Funds (since September 2013) and the Liquidity Funds and various money market funds (since May 2014) in the Fund Complex; Managing Director of the Adviser; Head of Public Markets Product Development (since 2006).
Timothy J. Knierim 522 Fifth Avenue New York, NY 10036 Birth Year 1959	Chief Compliance Officer	Since December 2016	Managing Director of the Adviser and various entities affiliated with the Adviser; Chief Compliance Officer of various Morgan Stanley Funds and the Adviser (since December 2016) and Chief Compliance Officer of Morgan Stanley AIP GP LP (since 2014). Formerly, Managing Director and Deputy Chief Compliance Officer of the Adviser (2014-2016); and formerly, Chief Compliance Officer of Prudential Investment Management, Inc. (2007-2014).
Francis J. Smith 522 Fifth Avenue New York, NY 10036 Birth Year 1965	Treasurer and Principal Financial Officer	Treasurer since July 2003 and Principal Financial Officer since September 2002	Managing Director of the Adviser and various entities affiliated with the Adviser; Treasurer (since July 2003) and Principal Financial Officer of various Morgan Stanley Funds (since September 2002).
Mary E. Mullin 522 Fifth Avenue New York, NY 10036 Birth Year 1967	Secretary	Since June 1999	Managing Director of the Adviser; Secretary of various Morgan Stanley Funds (since June 1999).
Michael J. Key 522 Fifth Avenue New York, NY 10036 Birth Year 1979	Vice President	Since June 2017	Vice President of the Equity and Fixed Income Funds, Liquidity Funds, various money market funds and the Morgan Stanley AIP Funds in the Fund Complex (since June 2017); Executive Director of the Adviser; Head of Product Development for Equity and Fixed Income Funds (since August 2013).

*  This is the earliest date the officer began serving the Morgan Stanley Funds. Each officer serves a one-year term, until his or her successor is elected and qualifies.

42

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Adviser and Administrator

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

Distributor

Morgan Stanley Distribution, Inc.
522 Fifth Avenue
New York, New York 10036

Dividend Disbursing and Transfer Agent

DST Asset Manager Solutions, Inc.
2000 Crown Colony Drive
Quincy, Massachusetts 02169

Custodian

State Street Bank and Trust Company
One Lincoln Street
Boston, Massachusetts 02111

Legal Counsel

Dechert LLP
1095 Avenue of the Americas
New York, New York 10036

Counsel to the Independent Trustees

Perkins Coie LLP
1155 Avenue of the Americas,
22nd Floor
New York, New York 10036

Independent Registered Public Accounting Firm

Ernst & Young LLP
200 Clarendon Street
Boston, Massachusetts 02116

Reporting to Shareholders

Each Morgan Stanley fund provides a complete schedule of portfolio holdings in its Semi-Annual and the Annual Reports within 60 days of the end of the fund's second and fourth fiscal quarters. The Semi-Annual and Annual Reports are filed electronically with the Securities and Exchange Commission ("SEC") on Form N-CSRS and Form N-CSR, respectively. Morgan Stanley also delivers the Semi-Annual and Annual Reports to fund shareholders and makes these reports available on its public website, www.morganstanley.com/im/shareholderreports. Each Morgan Stanley non-money market fund also files a complete schedule of portfolio holdings with the SEC for the fund's first and third fiscal quarters as an attachment to Form N-PORT. Morgan Stanley does not deliver the reports for the first and third fiscal quarters to shareholders, nor are the reports posted to the Morgan Stanley public website. However, the holdings for each money market fund are posted to the Morgan Stanley public website. You may obtain the Form N-PORT filings (as well as the Form N-CSR and N-CSRS filings) by accessing the SEC's website, www.sec.gov. You can also request copies of these materials, upon payment of a duplicating fee, by electronic request at the SEC's email address (publicinfo@sec.gov).

Proxy Voting Policies and Procedures and Proxy Voting Record

You may obtain a copy of the Trust's Proxy Voting Policy and Procedures and information regarding how the Trust voted proxies relating to portfolio securities during the most recent twelve-month period ended June 30, without charge, upon request, by calling toll free 1 (800) 548-7786 or by visiting our website at www.morganstanley.com/im/shareholderreports. This information is also available on the SEC's website at www.sec.gov.

This report is authorized for distribution only when preceded or accompanied by a prospectus or summary prospectus of the applicable fund of Morgan Stanley Institutional Fund Trust, which describes in detail the fund's investment policies, risks, fees and expenses. Please read the prospectus carefully before you invest or send money. For additional information, including information regarding the investments comprising the Fund, please visit our website at www.morganstanley.com/im/shareholderreports or call toll free 1 (800) 548-7786.

43

Printed in U.S.A.
This Report has been prepared for shareholders and may be distributed to others only if preceded or accompanied by a current prospectus.

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

© 2020 Morgan Stanley. Morgan Stanley Distribution, Inc.

IFTSIPANN
3298681 EXP 11.30.21

INVESTMENT MANAGEMENT

Morgan Stanley Institutional Fund Trust

Ultra-Short Income Portfolio

Annual Report

September 30, 2020

Beginning on January 1, 2021, as permitted by regulations adopted by the Securities and Exchange Commission ("SEC"), paper copies of the Fund's Annual and Semi-Annual Reports to Shareholders ("Shareholder Reports") will no longer be sent by mail, unless you specifically request paper copies of the Shareholder Reports from the Fund or from your financial intermediary, such as a broker-dealer or a bank. Instead, the Shareholder Reports will be made available on the Fund's website, https://www.morganstanley.com/im/shareholderreports and you will be notified by mail each time a Shareholder Report is posted and provided with a website link to access the Shareholder Report. If you already elected to receive Shareholder Reports electronically, you will not be affected by this change and you need not take any action. You may elect to receive Shareholder Reports and other communications from the Fund electronically anytime by contacting your financial intermediary or, if you are a direct investor, please follow the instructions on the envelope.

Beginning on January 1, 2019, you may elect to receive all future Shareholder Reports in paper free of charge. If you invest through a financial intermediary, you can contact your financial intermediary to request that you continue to receive paper copies of your Shareholder Reports. If you invest directly with the Fund, please follow the instructions on the envelope to let the Fund know you wish to continue receiving paper copies of your Shareholder Reports. Your election to receive Shareholder Reports in paper will apply to all funds held in your account if you invest through your financial intermediary or all funds held with the fund complex if you invest directly with a fund.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Table of Contents

Shareholders' Letter	2
Expense Example	3
Investment Overview	4
Portfolio of Investments	9
Statement of Assets and Liabilities	13
Statement of Operations	14
Statements of Changes in Net Assets	15
Financial Highlights	16
Notes to Financial Statements	19
Report of Independent Registered Public Accounting Firm	25
Investment Advisory Agreement Approval	26
Liquidity Risk Management Program	28
Privacy Notice	29
Trustee and Officer Information	31

This report is authorized for distribution only when preceded or accompanied by a prospectus or summary prospectus of the applicable Fund of the Morgan Stanley Institutional Fund Trust. To receive a prospectus and/or statement of additional information ("SAI"), which contains more complete information such as investment objectives, charges, expenses, policies for voting proxies, risk considerations and describes in detail each of the Fund's investment policies to the prospective investor, please call toll free 1 (800) 548-7786. Please read the prospectuses carefully before you invest or send money.

Additionally, you can access information about the Fund, including performance, characteristics and investment team commentary, through Morgan Stanley Investment Management's website: www.morganstanley.com/im/shareholderreports.

Market forecasts provided in this report may not necessarily come to pass. There is no guarantee that any sectors mentioned will continue to perform as discussed herein or that securities in such sectors will be held by the Fund in the future. There is no assurance that a fund will achieve its investment objective. Funds are subject to market risk, which is the possibility that market values of securities owned by the Fund will decline and, therefore, the value of the Fund's shares may be less than what you paid for them. Accordingly, you can lose money investing in this Fund. Please see the prospectus for more complete information on investment risks.

1

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Shareholders' Letter (unaudited)

Dear Shareholders,

We are pleased to provide this Annual Report, in which you will learn how your investment in Ultra-Short Income Portfolio (the "Fund") performed during the latest twelve-month period.

Morgan Stanley Investment Management is a client-centric, investor-led organization. Our global presence, intellectual capital, and breadth of products and services enable us to partner with investors to meet the evolving challenges of today's financial markets. We aim to deliver superior investment service and to empower our clients to make the informed decisions that help them reach their investment goals.

As always, we thank you for selecting Morgan Stanley Investment Management, and look forward to working with you in the months and years ahead.

Sincerely,

John H. Gernon
President and Principal Executive Officer

October 2020

2

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Expense Example (unaudited)

Ultra-Short Income Portfolio

As a shareholder of the Fund, you may incur two types of costs: (1) transactional costs; and (2) ongoing costs, which may include advisory fees, administration fees, distribution and shareholder services fees; and other Fund expenses. This example is intended to help you understand your ongoing costs (in dollars) of investing in the Fund and to compare these costs with the ongoing costs of investing in other mutual funds.

This example is based on an investment of $1,000 invested at the beginning of the six-month period ended September 30, 2020 and held for the entire six-month period.

Actual Expenses

The table below provides information about actual account values and actual expenses. You may use the information in this table, together with the amount you invested, to estimate the expenses that you paid over the period. Simply divide your account value by $1,000 (for example, an $8,600 account value divided by $1,000 = 8.6), then multiply the result by the number in the table under the heading entitled "Actual Expenses Paid During Period" to estimate the expenses you paid on your account during this period.

Hypothetical Example for Comparison Purposes

The table below provides information about hypothetical account values and hypothetical expenses based on the Fund's actual expense ratio and an assumed rate of return of 5% per year before expenses, which is not the Fund's actual return. The hypothetical account values and expenses may not be used to estimate the actual ending account balance or expenses you paid for the period. You may use this information to compare the ongoing costs of investing in the Fund and other funds. To do so, compare this 5% hypothetical example with the 5% hypothetical examples that appear in the shareholder reports of the other funds.

Please note that the expenses shown in the table are meant to highlight your ongoing costs only and do not reflect any transactional costs. Therefore, the information for each class in the table is useful in comparing ongoing costs only, and will not help you determine the relative total costs of owning different funds. In addition, if these transactional costs were included, your costs would have been higher.

	Beginning Account Value 4/1/20		Actual Ending Account Value 9/30/20		Hypothetical Ending Account Value		Actual Expenses Paid During Period*		Hypothetical Expenses Paid During Period*		Net Expense Ratio During Period**
Ultra-Short Income Portfolio Class IR	$	1,000.00	$	1,005.50	$	1,023.85	$	1.15	$	1.16		0.23	%
Ultra-Short Income Portfolio Institutional Class		1,000.00		1,006.30		1,023.60		1.40		1.42		0.28
Ultra-Short Income Portfolio Class A		1,000.00		1,005.50		1,022.90		2.11		2.12		0.42

*  Expenses are calculated using each Fund Class' annualized net expense ratio (as disclosed), multiplied by the average account value over the period and multiplied by 183/366 (to reflect the most recent one-half year period).

**  Annualized.

3

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Overview (unaudited)

Ultra-Short Income Portfolio

The Fund seeks current income with capital preservation while maintaining liquidity.

Performance

For the fiscal year ended September 30, 2020, the Fund's Institutional Share Class had a total return based on net asset value and reinvestment of distributions per share of 0.98%, net of fees. The Fund's Institutional Share Class underperformed against the Fund's benchmark, the ICE BofA 3-Month U.S. Treasury Bill Index (the "Index"), which returned 1.10%. For the seven-day period ended September 30, 2020, the Fund's Institutional Share Class provided an annualized current yield of 0.32% (subsidized) and 0.25% (non-subsidized), while its 30-day moving average annualized yield was 0.35% (subsidized) and 0.29% (non-subsidized). The 30-day SEC yield was 0.35% (subsidized) and 0.29% (non-subsidized). The non-subsidized yield reflects what the yield would have been had a fee and/or expense waiver not been in place during the period shown. Past performance is no guarantee of future results.

Factors Affecting Performance

•  At the September 2019 Federal Open Market Committee (FOMC or Committee) meeting, the Committee cut policy rates by 25 basis points to 1.75% to 2.00% as members "judged that downside risks to the outlook for economic activity had increased since their July meeting, particularly those stemming from trade policy uncertainty and conditions abroad." Separately, September 2019 witnessed a spike in overnight repo funding levels, which is not unusual given seasonal pressures related to corporate tax payments and the end of the quarter. However, a confluence of other factors such as the market absorbing an increased supply of Treasury securities after the recent lifting of the debt ceiling, exacerbated by lower bank reserves and tight bank balance sheets, raised the Secured Overnight Financing Rate as high as 5.25%.ⁱ The Federal Reserve (Fed) intervened with temporary open market operations and normalized the repo market for the remainder of September 2019.

•  Third quarter 2019 gross domestic product (GDP) expanded more than expected at a 2.6% annualized rate, largely due to strength in the consumer

spending sector, the biggest part of the economy.ⁱⁱ After an upward revision to 208,000 jobs created in September 2019, third quarter 2019 non-farm payrolls averaged 203,000, a promising sign that workers continue to find employment opportunities.ⁱⁱⁱ The jobless rate unexpectedly dropped 0.2% to 3.5% in September 2019, the lowest reading since December 1969.

•  As widely expected, the Fed cut interest rates for the third time in 2019 at its October FOMC meeting. In the prepared statement, the Committee dropped its pledge to "act as appropriate to sustain the expansion," while adding in promises to monitor incoming data as members "assess the appropriate path of the target for the federal funds rate." Changes to the statement suggested that policy makers were comfortable leaving interest rates on hold in the near term, while the market ended the month pricing in less than one additional rate cut over the next year. In addition, on October 11, 2019, the Fed announced that it would begin buying $60 billion of Treasury bills per month to improve its control over monetary policy, with a goal of expanding its balance sheet to $1.7 trillion by year-end 2019. While purely technical in nature, short-end Treasuries rallied on the back of the news, further flattening the yield curve. At the same time, the Fed also announced that it will "conduct term and overnight repurchase agreement operations at least through January of next year to ensure that the supply of reserves remains ample."

•  The Fed convened on December 10, 2019, for its last meeting of the calendar year. Chairman Powell and the FOMC voted to keep the federal funds rate unchanged at 1.50% to 1.75%. Chairman Powell signaled to the market that the Fed was comfortable with current policy and would take a "wait and see" approach going forward. The Federal Reserve press release stated that the current stance of monetary policy was appropriate to support economic expansion, strong labor markets and inflation near the FOMC's symmetric 2% objective. Overall, 2019 was eventful for the Fed and Chairman Powell. Entering 2019, investors expected rates to rise systematically during the year, but received quite the opposite policy action.

ⁱ  Source: Bloomberg L.P.

ⁱⁱ  Source for GDP data used in this report: Bureau of Economic Analysis and Bloomberg L.P.

ⁱⁱⁱ  Source for employment data used in this report: Bureau of Labor Statistics and Bloomberg L.P.

4

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Overview (unaudited) (cont'd)

Ultra-Short Income Portfolio

•  For the fourth quarter of 2019, GDP growth came in at 2.4% (annualized), slightly above market estimates. Personal spending and business investment were weaker, but GDP growth was aided by the housing market. Non-farm payrolls averaged 197,000 during the fourth quarter with the unemployment rate remaining low at 3.5% in December 2019.

•  On January 28, 2020, the Fed held its first policy meeting of the new decade. Although the federal funds rate was unchanged at 1.50% to 1.75%, policy committee members opted to increase the interest on excess reserves (IOER) rate by 5 basis points to 1.60%. The modification was a technical adjustment done in part to move the IOER rate closer to middle of the fed funds range from the lower end where it had trended in recent months. While most commentary was left unchanged in the accompanying press release, the Fed downgraded household spending from "strong" to "moderate." Similarly, the press release indicated that inflation needs to "return" to its 2% target rather than stay "near" the target, which had been used in previous press releases. Overall, the first meeting of 2020 was benign, as Chairman Powell viewed current policy as "appropriate." He reiterated that without any material change in the data going forward, policy was likely to remain unchanged. The January 2020 Fed statement did not address the emerging coronavirus epidemic, but Chairman Powell discussed the risk to the global economy in his press conference.

•  Throughout February 2020, investors flocked into relative safe-haven securities as fears of COVID-19 took center stage, sending the yield on the 10-year Treasury to its lowest level since 2016. In Europe, the entire German yield curve fell back below 0%. On February 25, 2020, the 10-year U.S. Treasury yield fell to a record low amid concern that the global spread of the virus was threatening supply chains critical to economic growth. The 30-year U.S. Treasury ended the month at record lows of 1.676%.^iv

•  As COVID-19 continued to spread rapidly around the world in early 2020, central bankers' fears

surrounding potential impacts began to materialize. Responding to the economic impact of the virus, the Fed conducted two unscheduled meetings in March 2020, which resulted in monetary easing and more accommodative monetary policy. The Fed lowered the target range for the federal funds rate to 0.00% to 0.25%. In addition to the rate cut, the Fed implemented several facilities to alleviate stresses in the marketplace. Most notably for short-term fixed income markets, these include the Money Market Mutual Fund Liquidity Facility (MMLF), Commercial Paper Funding Facility (CPFF) and Primary Dealer Credit Facility (PDCF). The Fed's overall goal was to ease the flow of credit across the broader fixed income markets and increase market confidence with their actions. Additionally, the FOMC announced an open-ended quantitative easing program that will increase its holdings of Treasury securities, agency mortgage-backed securities and commercial mortgage-backed securities in the amount needed to support the smooth functioning of these markets. The governmental actions taken, not only on the monetary side but also through fiscal stimulus aid, served to calm markets and support improved liquidity in the market.

•  First quarter 2020 GDP growth came in at –5.0% and initial jobless claims surged to around 30 million. While extraordinarily weak readings were anticipated as a result of the temporary pause across many parts of the economy, both data points underperformed expectations. Fed Chairman Powell noted in his press conference that the current policy was appropriate while acknowledging that "the ongoing public health crisis will weigh heavily on economic activity, employment and inflation in the near term, and poses considerable risks to the economic outlook over the medium term." The chairman also noted that the Committee will "maintain this target range until it is confident that the economy has weathered recent events."

•  At the April 29, 2020 meeting, the FOMC decided to keep the target range for the federal funds rate unchanged at 0.00% to 0.25%. This was the first

^iv  Source: Bloomberg L.P.

5

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Overview (unaudited) (cont'd)

Ultra-Short Income Portfolio

meeting since tangible economic data had been collected on the coronavirus impact. The Committee noted that the virus had catalyzed significant job losses and steep drawdowns in both consumer spending and consumer confidence.

•  As expected, the FOMC kept the range for the federal funds rate unchanged at 0.00% to 0.25% at the conclusion of its June 2020 meeting. The FOMC pledged to "continue to monitor the implications of incoming information for the economic outlook, including information related to public health, as well as global developments and muted inflation pressures, and will use its tools and act as appropriate to support the economy." The press release stated the FOMC will "increase its holdings" of Treasury securities and agency mortgage-backed securities at paces of $80 billion and $40 billion, respectively. However, publicizing the dollar figure diverges from previous meetings, which stated purchases would be conducted "in the amounts needed." In their updated dot plot, officials unanimously expected to keep rates at current levels through 2021, while 15 of the 17 officials expected rates to remain unchanged through 2022. As a result, the average federal funds forecast for 2020 and 2021 fell significantly.

•  Due to business shutdowns and stay-at-home orders, second quarter 2020 GDP contracted by –32.9%, the sharpest downturn since the 1940s. Personal spending fell by –34.5%, the largest slump on record. While the economic hit was well anticipated, the path of the recovery is linked to the complexity of the pandemic impact across the country. Ongoing unemployment benefits still remained high at 17 million at the end of July 2020, and the unemployment rate was at 10.2%. Personal spending has since improved, but uncertainty remained on how quickly and broadly the U.S. economy will fare in the second half of 2020.

•  In the July 2020 meeting, the FOMC kept the range for the federal funds rate unchanged at 0.00% to 0.25%. Although no structural policy changes were made in the month, the Fed extended the duration of its pandemic lending facilities such as the MMLF, PDCF and others to December 31, 2020. Many of the pandemic lending facilities were

set to expire at the end of September 2020. Economic activity and employment have "picked up somewhat," the July 2020 release noted, but such data are "well below" pre-pandemic levels. While Chairman Powell and the Committee acknowledged positive economic data, they believe the "path of the economy will depend significantly on the course of the virus." Going forward, the FOMC continued to pledge that it "will use its tools and act as appropriate to support the economy."

•  Minutes from the July 2020 FOMC meeting indicated that U.S. central bankers "agreed that the ongoing public health crisis would weigh heavily on economic activity, employment, and inflation in the near term and was posing considerable risks to the economic outlook over the medium term." Chairman Powell reiterated this sentiment when he said the path forward for the economy was "extraordinarily uncertain" and would remain dependent on containing the virus.

•  The annual Jackson Hole conference in August 2020 was notable in that Chairman Powell announced a new approach to monetary policy, one that takes a more relaxed stance on inflation and unemployment. A highlight from the released text indicated that the "Committee seeks to achieve inflation that averages 2% over time, and therefore judges that, following periods when inflation has been running persistently below 2%, appropriate monetary policy will likely aim to achieve inflation moderately above 2% for some time." In essence, the Fed has adopted a flexible form of average inflation targets as the key driver of monetary policy going forward.

•  Fed officials kept the benchmark policy rate unchanged at their September 2020 FOMC meeting, signaling they expect to maintain an accommodative stance of monetary policy until they achieve inflation averaging 2% over time and longer-term inflation expectations remain well anchored at 2%. The newly released dot plot showed that bankers expected near zero interest rates through 2023.

•  The portfolio's duration was favorable in a declining rate environment, which positively contributed to the net asset value (NAV) of the Fund.

6

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Overview (unaudited) (cont'd)

Ultra-Short Income Portfolio

•  However, the changing rate environment has negatively affected Fund performance from a yield perspective, given the lower reinvestment rates available as monetary policy remains near zero and the market has fully normalized post-March 2020 volatility.

•  Fund assets under management volatility and mark-to-market pricing in March 2020 put pressure on the NAV in the first half of 2020.

Management Strategies

•  Our investment philosophy continues to revolve around prudent credit, duration and risk management.

•  We continued to manage the Fund to minimize interest rate sensitivity in the changing rate environment.

•  We remain comfortable managing the portfolio with an excess amount of daily and weekly liquidity to help ensure we meet our mandates of capital preservation and liquidity.

•  Starting in the second quarter of 2020 and continuing through September 2020, we opportunistically extended the duration of the portfolio, remaining close to our Fund limit of 90 days weighted average maturity (WAM). Elevated WAM has enabled us to maintain what we consider to be cheap investments in the portfolio without worrying about the reset risk associated with floating-rate securities.

•  The weighted average life of the portfolio has rolled down to near 100 days as liquidity has risen and we focus on year-end maturities. Historically, the wholesale funding market experiences seasonal volatility in the fourth quarter, creating investment opportunities.

•  Exposure to LIBOR-based securities and inflows back into the Fund after the curve flattened in the third quarter of 2020 weighed on the yield of the portfolio, as attractive reinvestment options became scarce in the current zero interest rate environment.

•  At the end of the reporting period, portfolio composition remained high rated and liquid, focused on money market instruments, with no exposure to China and minimal amounts of asset-backed commercial paper.

•  A2/P2 rated bonds remained an attractive investment option, as they allowed us to diversify away from the financial sector that dominates the commercial paper/certificates of deposit market.^v As of the end of the reporting period, holdings in A2/P2 rated paper were below our typical 5% exposure, as supply has remained light and the spread between A1/P1 and A2/P2 remained extremely tight and not appropriate for the incremental risk, in our opinion.

^v  Diversification neither assures a profit nor guarantees against loss in a declining market.

7

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Overview (unaudited) (cont'd)

Ultra-Short Income Portfolio

*  Minimum Investment

**  Commenced operations on April 28, 2016.

In accordance with SEC regulations, the Fund's performance shown assumes and distributions were reinvested. The performance of Class A and Class IR shares will vary from the performance of Institutional Class shares and will be negatively impacted by additional fees assessed to those classes (where applicable).

Performance Compared to the ICE BofA 3-Month U.S. Treasury Bill Index⁽¹⁾, and the Lipper Ultra Short Obligations Funds Index⁽²⁾

	Period Ended September 30, 2020 Total Returns(3)
				Average Annual
	One Year			Five Years		Ten Years		Since Inception(5)
Fund — Class IR Shares w/o sales charges(4)		1.03	%		—		—		1.58	%
Fund — Institutional Class Shares w/o sales charges(4)		0.98			—		—		1.53
Fund — Class A Shares w/o sales charges(4)		0.80			—		—		1.33
ICE BofA 3-Month U.S. Treasury Bill Index		1.10			—		—		1.33
Lipper Ultra Short Obligations Funds Index		2.14			—		—		1.96

Performance data quoted represents past performance, which is no guarantee of future results, and current performance may be lower or higher than the figures shown. Performance assumes that all dividends and distributions, if any, were reinvested. For the most recent month-end performance figures, please visit www.morganstanley.com/im/shareholderreports. Investment returns and principal value will fluctuate so that Fund shares, when redeemed, may be worth more or less than their original cost. Total returns do not reflect the deduction of taxes that a shareholder would pay on Fund distributions or the redemption of Fund shares. Performance of share classes will vary due to differences in expenses.

⁽¹⁾  The ICE BofA (Intercontinental Exchange Bank of America) 3-Month U.S. Treasury Bill Index tracks the performance of U.S. Treasury bills with a remaining maturity of three months. The Index is unmanaged and its returns do not include any sales charges or fees. Such costs would lower performance. It is not possible to invest directly in an index.

⁽²⁾  The Lipper Ultra Short Obligations Funds Index is an equally weighted performance index of the largest qualifying funds (based on net assets) in the Lipper Ultra Short Obligations Funds classification. The Index, which is adjusted for capital gains distributions and income dividends, is unmanaged and should not be considered an investment. There are currently 30 funds represented in this Index. As of the date of this report, the Fund was in the Lipper Ultra Short Obligations' Funds classification.

⁽³⁾  Total returns for the Fund reflect expenses waived and/or reimbursed, if applicable, by the Adviser. Without such waivers and/or reimbursements, total returns would have been lower.

⁽⁴⁾  Commenced operations on April 28, 2016.

⁽⁵⁾  For comparative purposes, average annual since inception returns listed for the Indexes refer to the inception date of the Fund, not the inception of the Indexes.

8

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments

Ultra-Short Income Portfolio

	Face Amount (000)		Value (000)
Certificates of Deposit (20.6%)
Domestic Banks (2.7%)
Credit Suisse NY,
0.29%, 5/28/21	$	75,000	$	75,015
0.50%, 4/1/21		150,000		150,212
1.40%, 1/19/21		123,500		123,957
1.50%, 4/30/21		125,000		125,924
				475,108
International Banks (17.9%)
Banque Federative du Credit Mutuel SA
1.94%, 1/6/21		135,000		134,966
Barclays Bank PLC,
1.05%, 12/15/20 - 2/19/21		230,000		230,557
1.10%, 2/1/21		125,000		125,394
1.25%, 11/2/20		115,000		115,119
Canadian Imperial Bank of Commerce
0.43%, 8/3/21		205,000		205,338
Credit Industriel et Commercial,
1.88%, 1/19/21		175,000		174,943
1.93%, 1/29/21		200,000		199,922
Landesbank Hessen Thueringen
0.33%, 2/26/21		100,000		99,981
Lloyds Bank PLC
0.65%, 11/2/20		15,000		15,007
Mizuho Bank Ltd.
0.37%, 12/23/20		235,000		235,115
National Bank of Kuwait Sakp,
0.38%, 12/4/20		250,000		250,059
0.39%, 12/18/20		200,000		200,049
Qatar National Bank,
0.68%, 9/15/21		220,000		218,843
0.70%, 8/6/21		115,000		114,505
2.30%, 12/16/20 - 1/4/21		400,000		399,795
Societe Generale
0.10%, 10/6/20		175,000		175,000
UBS AG Stamford Branch,
1.51%, 1/7/21		150,000		150,541
1.54%, 2/8/21		150,000		150,722
				3,195,856
Total Certificates of Deposit (Cost $3,661,167)				3,670,964
Commercial Paper (a) (31.5%)
Asset-Backed Diversified Financial Services (5.0%)
Chesham Finance LLC,
0.12%, 10/1/20		450,000		449,999
0.14%, 10/2/20 - 10/9/20		400,000		399,995
Collateralized Commercial Paper FLEX Co. LLC
0.26%, 6/17/21		10,000		9,984
2.04%, 10/14/20		25,000		24,999
				884,977
Automobiles (0.8%)
Toyota Credit Canada, Inc.,
0.40%, 4/15/21 - 4/23/21		140,000		139,690

	Face Amount (000)		Value (000)
Consumer Non-Cyclical (4.6%)
LVMH Moet Hennessy Louis Vuitton Inc.,
0.33%, 8/9/21 - 8/11/21	$	180,000	$	179,719
0.35%, 7/12/21		105,000		104,856
0.37%, 12/22/20 - 12/24/20		285,000		284,916
0.38%, 7/12/21		135,000		134,815
0.50%, 12/21/20 (b)		125,000		124,965
				829,271
Diversified Financial Services (2.5%)
Barclays Bank PLC,
0.12%, 10/7/20 (b)		50,000		49,998
1.11%, 10/19/20 (b)		75,000		74,994
Intercontinental Exchange Inc.,
0.30%, 11/18/20 - 11/24/20		55,500		55,476
0.35%, 11/16/20		40,000		39,983
Jyske Bank A/S,
0.31%, 1/11/21 - 2/2/21		125,000		124,891
0.33%, 2/26/21 - 3/8/21		100,000		99,878
				445,220
Diversified Manufacturing (1.4%)
Honeywell International Inc.,
1.16%, 12/15/20		135,000		134,965
1.18%, 11/13/20 (b)		22,000		21,997
1.19%, 11/16/20		86,000		85,988
				242,950
Energy (4.1%)
Black Hills Corp.
0.12%, 10/1/20		4,000		4,000
Chevron Corp.
1.56%, 10/13/20		95,000		94,997
Exxon Mobil Corp.
1.99%, 10/16/20		80,000		79,997
Shell International Finance B.V.,
1.93%, 2/3/21		55,975		55,929
2.24%, 1/26/21 - 1/27/21		300,000		299,772
2.55%, 1/19/21		200,000		199,852
				734,547
Insurance (0.1%)
Pacific Life Short Term
0.22%, 10/16/20		1,400		1,400
Pricoa Short Term Funding LLC
0.28%, 6/7/21		12,000		11,990
Prudential Financial, Inc.
0.13%, 10/1/20		12,000		12,000
				25,390
International Banks (12.2%)
Barclays Bank PLC
0.40%, 2/5/21 (b)		175,000		174,885
BNG Bank NV
0.11%, 10/2/20		100,000		99,999

The accompanying notes are an integral part of the financial statements.
9

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Ultra-Short Income Portfolio

	Face Amount (000)		Value (000)
International Banks (cont'd)
BPCE SA,
0.29%, 6/4/21 (b)	$	250,000	$	249,614
0.46%, 3/19/21		160,000		159,859
DBS Group Holdings Ltd.
0.72%, 12/14/20		175,000		174,953
HSBC Bank PLC
0.60%, 5/18/21		50,000		49,921
Lloyds Bank PLC
0.35%, 12/1/20		92,000		91,981
Nationwide Building Society,
0.18%, 11/2/20 - 11/5/20		400,000		399,947
Societe Generale
0.08%, 10/1/20		290,000		289,999
Sumitomo Mitsui Trust Bank Ltd.,
0.41%, 12/22/20		225,000		224,920
0.43%, 12/18/20		75,000		74,975
Toronto Dominion Bank
0.08%, 10/1/20		180,000		179,999
				2,171,052
Wireless Telecommunications Services (0.8%)
AT&T, Inc.
1.47%, 12/18/20		150,000		149,894
Total Commercial Paper (Cost $5,616,504)				5,622,991
Corporate Bonds (6.0%)
Diversified Financial Services (0.7%)
Citigroup, Inc.,
2.35%, 8/2/21		6,806		6,923
2.70%, 3/30/21		26,519		26,835
JPMorgan Chase & Co.,
2.55%, 3/1/21		45,609		45,953
4.63%, 5/10/21		9,150		9,392
Sumitomo Mitsui Financial Group, Inc.,
2.06%, 7/14/21		13,592		13,780
2.93%, 3/9/21		19,216		19,432
				122,315
Domestic Banks (4.1%)
Bank of America Corp.,
2.63%, 10/19/20 - 4/19/21		71,691		72,474
Bank of New York Mellon Corp. (The)
2.05%, 5/3/21		3,983		4,020
Wells Fargo & Co.,
2.10%, 7/26/21		256,632		260,294
2.50%, 3/4/21		161,215		162,717
3.00%, 1/22/21		58,816		59,320
4.60%, 4/1/21		167,024		170,580
				729,405
International Banks (1.2%)
BPCE SA
2.65%, 2/3/21		6,600		6,653
Credit Industriel et Commercial
1.88%, 12/18/20		200,000		199,965

	Face Amount (000)		Value (000)
Mizuho Financial Group, Inc.,
2.27%, 9/13/21	$	8,711	$	8,872
2.63%, 4/12/21 (b)		5,275		5,340
				220,830
Total Corporate Bonds (Cost $1,070,846)				1,072,550
Floating Rate Notes (c) (21.6%)
Automobiles (0.6%)
Toyota Motor Credit Corp., SOFR + 0.40%
0.48%, 10/23/20		113,000		113,025
Diversified Financial Services (0.1%)
Sumitomo Mitsui Financial Group, Inc.,
3 Month USD LIBOR + 1.11%, 1.38%, 7/14/21		9,353		9,427
3 Month USD LIBOR + 1.68%, 1.92%, 3/9/21		5,642		5,681
				15,108
Domestic Banks (4.5%)
Bank of America Corp.,
3 Month USD LIBOR + 1.42%, 1.69%, 4/19/21		10,750		10,831
First Abu Dhabi Bank USA,
3 Month USD LIBOR + 0.20%, 1.31%, 1/21/21		250,000		250,049
HSBC Bank USA NA,
3 Month USD LIBOR + 0.38%, 0.65%, 4/29/21		100,000		100,198
ING U.S. Funding LLC,
3 Month USD LIBOR + 0.20%, 0.47%, 10/19/20 (b)		100,000		100,009
Mizuho Securities USA LLC,
3 Month USD LIBOR + 0.16%, 0.41%, 9/27/21 (b)		50,000		50,008
1 Month USD LIBOR + 0.28%, 0.43%, 2/16/21		51,000		51,037
3 Month USD LIBOR + 0.19%, 0.47%, 8/23/21		85,000		85,012
Wells Fargo & Co.,
3 Month USD LIBOR + 1.03%, 1.27%, 7/26/21		122,318		123,226
3 Month USD LIBOR + 1.34%, 1.59%, 3/4/21		23,558		23,682
				794,052
Insurance (0.1%)
Metropolitan Life Global Funding I,
SOFR + 0.50%, 0.58%, 5/28/21 (b)		25,000		25,045
International Banks (16.3%)
Bank of Montreal,
3 Month USD LIBOR + 0.13%, 0.43%, 7/6/21		30,000		30,028
BNZ International Funding Ltd.,
1 Month USD LIBOR + 0.27%, 0.41%, 10/27/20 (b)		140,000		140,029
3 Month USD LIBOR + 0.19%, 0.47%, 10/8/20 (b)		125,000		125,005

The accompanying notes are an integral part of the financial statements.
10

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Ultra-Short Income Portfolio

	Face Amount (000)		Value (000)
International Banks (cont'd)
Canadian Imperial Bank of Commerce,
3 Month USD LIBOR + 0.16%, 0.40%, 8/6/21	$	150,000	$	150,197
Credit Suisse AG,
3 Month USD LIBOR + 0.23%, 0.47%, 12/30/20		300,000		300,167
Gilead Sciences, Inc.,
3 Month USD LIBOR + 0.15%, 0.36%, 9/17/21		40,000		40,002
HSBC Bank PLC,
1 Month USD LIBOR + 0.40%, 0.55%, 10/6/20 (b)		195,000		195,014
3 Month USD LIBOR + 0.40%, 0.65%, 4/28/21 (b)		100,000		100,208
Lloyds Bank PLC,
1 Month USD LIBOR + 0.17%, 0.32%, 12/4/20 (b)		115,000		115,033
Mizuho Financial Group, Inc.,
3 Month USD LIBOR + 1.14%, 1.39%, 9/13/21		10,320		10,416
3 Month USD LIBOR + 1.48%, 1.75%, 4/12/21 (b)		9,000		9,065
Skandinaviska Enskilda Banken AB,
3 Month USD LIBOR + 0.15%, 0.45%, 10/5/20		195,000		195,003
Societe Generale,
3 Month USD LIBOR + 0.23%, 0.48%, 2/2/21 (b)		165,000		165,086
3 Month USD LIBOR + 0.25%, 0.49%, 12/14/20 (b)		250,000		250,124
Sumitomo Mitsui Banking Corp.,
3 Month USD LIBOR + 0.35%, 0.62%, 7/16/21		17,610		17,645
0.66%, 4/6/21		131,391		131,615
Svenska Handelsbanken,
3 Month USD LIBOR + 0.15%, 0.37%, 12/30/20		200,000		200,091
3 Month USD LIBOR + 0.15%, 0.45%, 10/2/20		75,000		75,000
Toronto-Dominion Bank,
3 Month USD LIBOR + 0.19%, 0.47%, 10/7/20		75,000		75,003
Toyota Motor Finance,
3 Month USD LIBOR + 0.10%, 0.35%, 6/8/21		195,000		195,020
UBS AG London,
3 Month USD LIBOR + 0.18%, 0.40%, 6/25/21 (b)		390,000		390,273
				2,910,024
Total Floating Rate Notes (Cost $3,855,332)				3,857,254

	Face Amount (000)		Value (000)
Repurchase Agreements (14.7%)
ABN Amro Securities LLC, (0.28%, dated 9/30/20, due 10/1/20; proceeds $1,000; fully collateralized by various Corporate Bonds; 1.66% - 6.63% due 9/1/21 - 9/1/50; valued at $1,043)	$	1,000	$	1,000
Bank of America Securities, Inc., (0.40% (c), dated 9/2/20, due 12/4/20; proceeds $175,181; fully collateralized by various Common Stocks and Preferred Stocks; valued at $183,750) (Demand 10/02/20) (d)		175,000		175,000
Bank of America Securities, Inc., (0.55% (c), dated 7/27/20, due 7/27/21; proceeds $301,673; fully collateralized by various Common Stocks and Preferred Stocks; valued at $317,047) (Demand 10/27/20) (d)		300,000		300,000
BMO Capital Markets Corp., (0.21%, dated 9/30/20, due 10/1/20; proceeds $1,000; fully collateralized by various Corporate Bonds; 2.65% - 3.50% due 9/22/21 - 9/13/23; valued at $1,051)		1,000		1,000
BNP Paribas Prime Brokerage, Inc., (0.38%, dated 9/30/20, due 10/1/20; proceeds $190,002; fully collateralized by various Corporate Bonds; 2.31% - 12.00% due 6/12/21 - 10/7/79; valued at $201,006) (d)		190,000		190,000
BNP Paribas Securities Corp., (0.48%, dated 9/21/20, due 12/21/20; proceeds $200,243; fully collateralized by various Corporate Bonds; 3.88% - 11.50% due 6/15/21 - 11/1/48; valued at $211,796) (d)		200,000		200,000
Credit Agricole Corporate and Investment Bank, (0.22%, dated 9/17/20, due 10/19/20; proceeds $50,010; fully collateralized by various Corporate Bonds; 3.2% - 4.1% due 6/20/23 - 3/26/25; valued at $52,500) (Demand 10/07/20)		50,000		50,000
Credit Agricole Corporate and Investment Bank, (0.22%, dated 9/30/20, due 10/26/20; proceeds $100,016; fully collateralized by various Corporate Bonds; 2.05% - 4.27% due 11/10/20 - 2/21/30; valued at $105,001) (Demand 10/07/20)		100,000		100,000
Credit Agricole Corporate and Investment Bank, (0.24%, dated 8/11/20, due 11/12/20; proceeds $200,124; fully collateralized by various Corporate Bonds;1.02% - 5.88% due 9/11/22 - 5/8/30; valued at $210,000) (Demand 10/07/20)		200,000		200,000
JP Morgan Securities LLC, (0.46% (c), dated 8/17/20, due 12/4/20; proceeds $250,348; fully collateralized by various Common Stocks and Preferred Stocks; valued at $262,601) (Demand 10/1/20) (d)		250,000		250,000

The accompanying notes are an integral part of the financial statements.
11

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Ultra-Short Income Portfolio

	Face Amount (000)		Value (000)
Repurchase Agreements (cont'd)
JP Morgan Securities LLC, (0.46% (c), dated 9/1/20, due 12/4/20; proceeds $100,120; fully collateralized by various Common Stocks and Preferred Stocks; valued at $105,040) (Demand 10/01/20) (d)	$	100,000	$	100,000
Mizuho Securities USA LLC, (0.23%, dated 9/30/20, due 10/1/20; proceeds $5,000; fully collateralized by various Common Stocks and Preferred Stocks; valued at $5,250) (d)		5,000		5,000
Pershing LLC, (0.40%, dated 9/30/20 due 10/1/20; proceeds $100,001; fully collateralized by various Corporate Bonds; 0.43% - 10.88% due 12/14/20 - 3/1/68; valued at $105,797) (d)		100,000		100,000
Scotia Capital USA, Inc., (0.33%, dated 9/30/20, due 10/1/20; proceeds $30,000; fully collateralized by various Corporate Bonds; 0.75% - 4.75% due 6/10/25 - 6/15/50; valued at $31,500)		30,000		30,000
Scotia Capital USA, Inc., (0.43%, dated 9/30/20, due 10/1/20; proceeds $850,010; fully collateralized by various Corporate Bonds; 3.55% - 9.25% due 10/26/20 - 10/15/27; valued at $900,883)		850,000		850,000
Wells Fargo Securities LLC, (0.55%, dated 9/9/20, due 12/7/20; proceeds $80,109; fully collateralized by various Common Stocks and Preferred Stocks; valued at $84,000) (d)		80,000		80,000
Total Repurchase Agreements (Cost $2,632,000)				2,632,000
Time Deposits (5.6%)
Domestic Bank (4.6%)
National Bank of Canada (Montreal Branch)
0.09%, 10/1/20		820,000		820,000
				820,000
International Banks (1.0%)
Canadian Imperial Bank of Commerce
0.08%, 10/1/20		100,000		100,000
Credit Agricole Corporate and Investment Bank
0.08%, 10/1/20		86,000		86,000
Total International Banks (Cost $186,000)				186,000
Total Time Deposits (Cost $1,006,000)				1,006,000
Total Investments (100.0%) (Cost $17,841,849) (e)				17,861,759
Liabilities in Excess of Other Assets (0.0%) (f)				(4,616	)
Net Assets (100.0%)			$	17,857,143

(a)  The rates shown are the effective yields at the date of purchase.

(b)  144A security — Certain conditions for public sale may exist. Unless otherwise noted, these securities are deemed to be liquid.

(c)  Floating or variable rate securities: The rates disclosed are as of September 30, 2020. For securities based on a published reference rate and spread, the reference rate and spread are indicated in the description in the Portfolio of Investments. Certain variable rate securities may not be based on a published reference rate and spread but are determined by the issuer or agent and are based on current market conditions. These securities do not indicate a reference rate and spread in their description in the Portfolio of Investments.

(d)  Perpetual — One or more securities do not have a predetermined maturity date. Rates for these securities are fixed for a period of time, after which they revert to a floating rate. Interest rates in effect are as of September 30, 2020.

(e)  At September 30, 2020, the aggregate cost for federal income tax purposes is approximately $17,841,849,000. The aggregate gross unrealized appreciation is approximately $19,925,000 and the aggregate gross unrealized depreciation is approximately $15,000, resulting in net unrealized appreciation of approximately $19,910,000.

(f)  Amount is less than 0.05%.

LIBOR  London Interbank Offered Rate.

SOFR  Secured Overnight Financing Rate.

USD  United States Dollar.

Portfolio Composition

Classification	Percentage of Total Investments
Commercial Paper		31.5	%
Floating Rate Notes		21.6
Certificates of Deposit		20.6
Repurchase Agreements		14.7
Corporate Bonds		6.0
Time Deposits		5.6
Total Investments		100.0	%

The accompanying notes are an integral part of the financial statements.
12

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Ultra-Short Income Portfolio

Statement of Assets and Liabilities	September 30, 2020 (000)
Assets:
Investments in Securities of Unaffiliated Issuers, at Value (Cost $17,841,849, including value of repurchases agreements of $2,632,000)	$	17,861,759
Cash		405
Receivable for Fund Shares Sold		58,483
Interest Receivable		16,964
Other Assets		1,565
Total Assets		17,939,176
Liabilities:
Payable for Fund Shares Redeemed		72,745
Payable for Advisory Fees		5,911
Payable for Shareholder Services Fees — Institutional Class		106
Payable for Shareholder Services Fees — Class A		1,230
Payable for Administration Fees		1,191
Dividends Payable		256
Payable for Custodian Fees		88
Payable for Professional Fees		63
Payable for Transfer Agency Fees — Class IR		11
Payable for Transfer Agency Fees — Institutional Class		3
Payable for Transfer Agency Fees — Class A		2
Other Liabilities		427
Total Liabilities		82,033
Net Assets	$	17,857,143
Net Assets Consist of:
Paid-in-Capital	$	17,903,049
Total Accumulated Loss		(45,906	)
Net Assets	$	17,857,143
CLASS IR:
Net Assets	$	5,388,750
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		539,531,162
Net Asset Value, Offering and Redemption Price Per Share	$	9.99
Institutional Class:
Net Assets	$	2,544,657
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		254,801,472
Net Asset Value, Offering and Redemption Price Per Share	$	9.99
CLASS A:
Net Assets	$	9,923,736
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		993,748,846
Net Asset Value, Offering and Redemption Price Per Share	$	9.99

The accompanying notes are an integral part of the financial statements.
13

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Ultra-Short Income Portfolio

Statement of Operations	Year Ended September 30, 2020 (000)
Investment Income:
Interest from Securities of Unaffiliated Issuers	$	284,316
Expenses:
Advisory Fees (Note B)		35,113
Shareholder Services Fees — Institutional Class (Note D)		1,424
Shareholder Services Fees — Class A (Note D)		25,276
Administration Fees (Note C)		14,045
Registration Fees		3,180
Custodian Fees (Note F)		393
Trustees' Fees and Expenses		339
Professional Fees		168
Shareholder Reporting Fees		157
Transfer Agency Fees — Class IR (Note E)		43
Transfer Agency Fees — Institutional Class (Note E)		11
Transfer Agency Fees — Class A (Note E)		8
Pricing Fees		16
Other Expenses		479
Expenses Before Non Operating Expenses		80,652
Bank Overdraft Expense		1
Total Expenses		80,653
Waiver of Advisory Fees (Note B)		(12,455	)
Reimbursement of Class Specific Expenses — Class IR (Note B)		(49	)
Reimbursement of Class Specific Expenses — Institutional Class (Note B)		(12	)
Waiver of Shareholder Servicing Fees — Class A (Note D)		(2,447	)
Net Expenses		65,690
Net Investment Income		218,626
Realized Loss:
Investments Sold		(67,256	)
Change in Unrealized Appreciation (Depreciation):
Investments		7,979
Net Realized Loss and Change in Unrealized Appreciation (Depreciation)		(59,277	)
Net Increase in Net Assets Resulting from Operations	$	159,349

The accompanying notes are an integral part of the financial statements.
14

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Ultra-Short Income Portfolio

Statements of Changes in Net Assets	Year Ended September 30, 2020 (000)			Year Ended September 30, 2019 (000)
Increase (Decrease) in Net Assets:
Operations:
Net Investment Income	$	218,626		$	351,961
Net Realized Gain (Loss)		(67,256	)		769
Net Change in Unrealized Appreciation		7,979			8,581
Net Increase in Net Assets Resulting from Operations		159,349			361,311
Dividends and Distributions to Shareholders:
Class IR		(61,803	)		(81,786	)
Institutional Class		(39,633	)		(71,086	)
Class A		(117,190	)		(199,089	)
Total Dividends and Distributions to Shareholders		(218,626	)		(351,961	)
Capital Share Transactions:(1)
Class IR:
Subscribed		9,745,593			7,672,933
Distributions Reinvested		49,827			71,902
Redeemed		(9,159,258	)		(4,822,141	)
Institutional Class:
Subscribed		4,112,421			3,028,912
Distributions Reinvested		39,629			71,086
Redeemed		(4,681,680	)		(2,739,398	)
Class A:
Subscribed		12,175,182			12,220,046
Distributions Reinvested		117,124			198,964
Redeemed		(13,117,055	)		(7,906,616	)
Net Increase (Decrease) in Net Assets Resulting from Capital Share Transactions		(718,217	)		7,795,688
Total Increase (Decrease) in Net Assets		(777,494	)		7,805,038
Net Assets:
Beginning of Period		18,634,637			10,829,599
End of Period	$	17,857,143		$	18,634,637
(1)   Capital Share Transactions:
Class IR:
Shares Subscribed		974,475			765,985
Shares Issued on Distributions Reinvested		4,979			7,177
Shares Redeemed		(915,518	)		(481,379	)
Net Increase in Class IR Shares Outstanding		63,936			291,783
Institutional Class:
Shares Subscribed		410,877			302,377
Shares Issued on Distributions Reinvested		3,960			7,097
Shares Redeemed		(468,012	)		(273,488	)
Net Increase (Decrease) in Institutional Class Shares Outstanding		(53,175	)		35,986
Class A:
Shares Subscribed		1,217,011			1,220,000
Shares Issued on Distributions Reinvested		11,703			19,862
Shares Redeemed		(1,311,473	)		(789,334	)
Net Increase (Decrease) in Class A Shares Outstanding		(82,759	)		450,528

The accompanying notes are an integral part of the financial statements.
15

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Ultra-Short Income Portfolio

	Class IR
	Year Ended September 30,												Period from April 28, 2016(1) to
Selected Per Share Data and Ratios	2020			2019			2018			2017			September 30, 2016
Net Asset Value, Beginning of Period	$	10.02		$	10.01		$	10.01		$	10.00		$	10.00
Income (Loss) from Investment Operations:
Net Investment Income(2)		0.13			0.25			0.19			0.12			0.03
Net Realized and Unrealized Gain (Loss)		(0.03	)		0.01			(0.01	)		0.00	(3)		0.00	(3)
Total from Investment Operations		0.10			0.26			0.18			0.12			0.03
Distributions from and/or in Excess of:
Net Investment Income		(0.13	)		(0.25	)		(0.18	)		(0.11	)		(0.03	)
Net Realized Gain		—			—			(0.00	)(3)		(0.00	)(3)		—
Total Distributions		(0.13	)		(0.25	)		(0.18	)		(0.11	)		(0.03	)
Net Asset Value, End of Period	$	9.99		$	10.02		$	10.01		$	10.01		$	10.00
Total Return(4)		1.03	%		2.68	%		1.87	%		1.18	%		0.26	%(5)
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	5,388,750		$	4,765,201		$	1,840,647		$	1,122,452		$	276,348
Ratio of Expenses Before Expense Limitation		0.31	%		0.30	%		0.30	%		0.30	%		0.42	%(6)
Ratio of Expenses After Expense Limitation		0.24	%		0.24	%		0.23	%		0.22	%		0.18	%(6)
Ratio of Expenses After Expense Limitation Excluding Non-Operating Expenses		0.24	%		0.24	%		N/A			N/A			N/A
Ratio of Net Investment Income		1.34	%		2.53	%		1.86	%		1.16	%		0.61	%(6)
Portfolio Turnover Rate		N/A(7)			N/A(7)			N/A(7)			N/A(7)			N/A(7)

(1)  Commencement of Operations.

(2)  Per share amount is based on average shares outstanding.

(3)  Amount is less than $0.005 per share.

(4)  Calculated based on the net asset value as of the last business day of the period.

(5)  Not annualized.

(6)  Annualized.

(7)  During the reporting period, the Fund did not hold any long-term investments and accordingly portfolio turnover is not applicable.

The accompanying notes are an integral part of the financial statements.
16

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Ultra-Short Income Portfolio

	Institutional Class
	Year Ended September 30,												Period from April 28, 2016(1) to
Selected Per Share Data and Ratios	2020			2019			2018			2017			September 30, 2016
Net Asset Value, Beginning of Period	$	10.02		$	10.01		$	10.01		$	10.00		$	10.00
Income (Loss) from Investment Operations:
Net Investment Income(2)		0.14			0.25			0.18			0.11			0.02
Net Realized and Unrealized Gain (Loss)		(0.04	)		0.01			0.00	(3)		0.00	(3)		0.00	(3)
Total from Investment Operations		0.10			0.26			0.18			0.11			0.02
Distributions from and/or in Excess of:
Net Investment Income		(0.13	)		(0.25	)		(0.18	)		(0.10	)		(0.02	)
Net Realized Gain		—			—			(0.00	)(3)		(0.00	)(3)		—
Total Distributions		(0.13	)		(0.25	)		(0.18	)		(0.10	)		(0.02	)
Net Asset Value, End of Period	$	9.99		$	10.02		$	10.01		$	10.01		$	10.00
Total Return(4)		0.98	%		2.62	%		1.82	%		1.13	%		0.24	%(5)
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	2,544,657		$	3,085,210		$	2,722,775		$	1,695,589		$	196,092
Ratio of Expenses Before Expense Limitation		0.36	%		0.34	%		0.35	%		0.35	%		0.48	%(6)
Ratio of Expenses After Expense Limitation		0.29	%		0.29	%		0.28	%		0.27	%		0.23	%(6)
Ratio of Expenses After Expense Limitation Excluding Non-Operating Expenses		0.29	%		0.29	%		N/A			N/A			N/A
Ratio of Net Investment Income		1.39	%		2.48	%		1.84	%		1.09	%		0.65	%(6)
Portfolio Turnover Rate		N/A(7)			N/A(7)			N/A(7)			N/A(7)			N/A(7)

(1)  Commencement of Operations.

(2)  Per share amount is based on average shares outstanding.

(3)  Amount is less than $0.005 per share.

(4)  Calculated based on the net asset value as of the last business day of the period.

(5)  Not annualized.

(6)  Annualized.

(7)  During the reporting period, the Fund did not hold any long-term investments and accordingly portfolio turnover is not applicable.

The accompanying notes are an integral part of the financial statements.
17

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Ultra-Short Income Portfolio

	Class A
	Year Ended September 30,												Period from April 28, 2016(1) to
Selected Per Share Data and Ratios	2020			2019			2018			2017			September 30, 2016
Net Asset Value, Beginning of Period	$	10.02		$	10.01		$	10.01		$	10.00		$	10.00
Income (Loss) from Investment Operations:
Net Investment Income(2)		0.12			0.23			0.17			0.09			0.01
Net Realized and Unrealized Gain (Loss)		(0.04	)		0.01			(0.01	)		0.00	(3)		0.00	(3)
Total from Investment Operations		0.08			0.24			0.16			0.09			0.01
Distributions from and/or in Excess of:
Net Investment Income		(0.11	)		(0.23	)		(0.16	)		(0.08	)		(0.01	)
Net Realized Gain		—			—			(0.00	)(3)		(0.00	)(3)		—
Total Distributions		(0.11	)		(0.23	)		(0.16	)		(0.08	)		(0.01	)
Net Asset Value, End of Period	$	9.99		$	10.02		$	10.01		$	10.01		$	10.00
Total Return(4)		0.80	%		2.42	%		1.61	%		0.92	%		0.14	%(5)
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	9,923,736		$	10,784,226		$	6,266,177		$	2,581,479		$	164,528
Ratio of Expenses Before Expense Limitation		0.56	%		0.55	%		0.55	%		0.55	%		0.68	%(6)
Ratio of Expenses After Expense Limitation		0.46	%		0.49	%		0.48	%		0.47	%		0.44	%(6)
Ratio of Expenses After Expense Limitation Excluding Non-Operating Expenses		0.46	%		0.49	%		N/A			N/A			N/A
Ratio of Net Investment Income		1.16	%		2.29	%		1.68	%		0.91	%		0.48	%(6)
Portfolio Turnover Rate		N/A(7)			N/A(7)			N/A(7)			N/A(7)			N/A(7)

(1)  Commencement of Operations.

(2)  Per share amount is based on average shares outstanding.

(3)  Amount is less than $0.005 per share.

(4)  Calculated based on the net asset value as of the last business day of the period.

(5)  Not annualized.

(6)  Annualized.

(7)  During the reporting period, the Fund did not hold any long-term investments and accordingly portfolio turnover is not applicable.

The accompanying notes are an integral part of the financial statements.
18

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements

Morgan Stanley Institutional Fund Trust ("Trust'') is registered under the Investment Company Act of 1940, as amended (the "Act''), as an open-end management investment company. The Trust is comprised of twelve separate, active funds (individually referred to as a "Fund," collectively as the "Funds"). The Trust applies investment company accounting and reporting guidance. All Funds are considered diversified for purposes of the Act.

The accompanying financial statements relate to the Ultra-Short Income Portfolio. The Fund seeks current income with capital preservation while maintaining liquidity. The Fund offers three classes of shares — Class IR, Institutional Class and Class A.

A. Significant Accounting Policies: The following significant accounting policies are in conformity with U.S. generally accepted accounting principles ("GAAP"). Such policies are consistently followed by the Trust in the preparation of its financial statements. GAAP may require management to make estimates and assumptions that affect the reported amounts and disclosures in the financial statements. Actual results may differ from those estimates.

In March 2017, the Financial Accounting Standards Board ("FASB") issued an Accounting Standard Update, ASU 2017-08, Receivables-Nonrefundable Fees and Other Costs (Subtopic 310-20), Premium Amortization on Purchased Callable Debt Securities (the "ASU") which amends the amortization period for certain purchased callable debt securities held at a premium, shortening such period to the earliest call date. The ASU does not require any accounting change for debt securities held at a discount; the discount continues to be amortized to maturity. The ASU is effective for fiscal years, and interim periods within those fiscal years, beginning after December 15, 2018. The Fund has adopted the ASU as of September 30, 2020 and it did not have an impact on the Fund's financial statements.

In March 2020, FASB issued an Accounting Standard Update, ASU 2020-04, Reference Rate Reform (Topic 848) — Facilitation of the Effects of Reference Rate Reform on Financial Reporting ("ASU 2020-04"), which provides optional, temporary relief with respect to the financial reporting of contracts subject to certain types of modifications due to the planned discontinuation of the London Interbank Offered Rate ("LIBOR") and other IBOR-based reference rates at the end of 2021. The temporary relief provided by ASU 2020-04 is effective for certain reference rate-related contract

modifications that occur during the period from March 12, 2020 through December 31, 2022. Management is evaluating the impact of ASU 2020-04 on the Fund's investments, derivatives, debt and other contracts that will undergo reference rate-related modifications as a result of the reference rate reform.

1.  Security Valuation: (1) Certain portfolio securities may be valued by an outside pricing service/vendor approved by the Trust's Board of Trustees (the "Trustees"). The pricing service/vendor may employ a pricing model that takes into account, among other things, bids, yield spreads and/or other market data and specific security characteristics. Alternatively, if a valuation is not available from an outside pricing service/vendor, and the security trades on an exchange, the security may be valued at its latest reported sale price (or at the exchange official closing price if such exchange reports an official closing price), prior to the time when assets are valued. If there are no sales on a given day and if there is no official exchange closing price for that day, the security is valued at the mean between the last reported bid and asked prices if such bid and asked prices are available in the relevant exchanges. If only bid prices are available then the latest bid price may be used. If Morgan Stanley Investment Management Inc. (the "Adviser"), a wholly-owned subsidiary of Morgan Stanley, determines that the price provided by the outside pricing service/vendor or exchange does not reflect the security's fair value or is unable to provide a price, prices from brokers or dealers may also be utilized. In these circumstances, the value of the security will be the mean of bid and asked prices obtained from brokers or dealers; and (2) when market quotations are not readily available, including circumstances under which the Adviser determines that the closing price, last sale price or the mean between the last reported bid and asked prices are not reflective of a security's market value, portfolio securities are valued at their fair value as determined in good faith under procedures established by and under the general supervision of the Trustees. Occasionally, developments affecting the closing prices of securities and other assets may occur between the times at which valuations of such securities are determined (that is, close of the foreign market on which the securities trade) and the close of business of the New York Stock Exchange ("NYSE"). If developments occur during such periods that are expected to materially affect the value of such securities, such valuations may be adjusted to reflect the estimated fair value of such securities

19

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

as of the close of the NYSE, as determined in good faith by the Trustees or by the Adviser using a pricing service and/or procedures approved by the Trustees.

The Trustees have responsibility for determining in good faith the fair value of the investments, and the Trustees may appoint others, such as the Trust's Adviser or a valuation committee, to assist the Trustees in determining fair value and to make the actual calculations pursuant to the fair valuation methodologies previously approved by the Trustees. Under procedures approved by the Trustees, the Trust's Adviser has formed a Valuation Committee whose members are approved by the Trustees. The Valuation Committee provides administration and oversight of the Trust's valuation policies and procedures, which are reviewed at least annually by the Trustees. These procedures allow the Trust to utilize independent pricing services, quotations from securities and financial instrument dealers and other market sources to determine fair value.

2.  Fair Value Measurement: FASB Accounting Standards Codification^TM ("ASC") 820, "Fair Value Measurement" ("ASC 820"), defines fair value as the value that the Fund would receive to sell an investment or pay to transfer a liability in a timely transaction with an independent buyer in the principal market, or in the absence of a principal market, the most advantageous market for the investment or liability. ASC 820 establishes a three-tier hierarchy to distinguish between (1) inputs that reflect the assumptions market participants would use in valuing an asset or liability developed based on market data obtained from sources independent of the reporting entity (observable inputs) and (2) inputs that reflect the reporting entity's own assumptions about the assumptions market participants would use in valuing an asset or liability developed based on the best information available in the circumstances (unobservable inputs) and to establish classification of fair value measurements for disclosure purposes. Various inputs are used in determining the value of the Fund's investments. The inputs are summarized in the three broad levels listed below:

•  Level 1 – unadjusted quoted prices in active markets for identical investments

•  Level 2 – other significant observable inputs (including quoted prices for similar investments,

interest rates, prepayment speeds, credit risk, etc.)

•  Level 3 – significant unobservable inputs including the Fund's own assumptions in determining the fair value of investments. Factors considered in making this determination may include, but are not limited to, information obtained by contacting the issuer, analysts, or the appropriate stock exchange (for exchange-traded securities), analysis of the issuer's financial statements or other available documents and, if necessary, available information concerning other securities in similar circumstances.

The inputs or methodology used for valuing securities are not necessarily an indication of the risk associated with investing in those securities and the determination of the significance of a particular input to the fair value measurement in its entirety requires judgment and considers factors specific to each security.

The following is a summary of the inputs used to value the Fund's investments as of September 30, 2020:

Investment Type	Level 1 Unadjusted quoted prices (000)		Level 2 Other significant observable inputs (000)		Level 3 Significant unobservable inputs (000)		Total (000)
Assets:
Short-Term Investments
Certificates of Deposit	$	—	$	3,670,964	$	—	$	3,670,964
Commercial Paper		—		5,622,991		—		5,622,991
Corporate Bonds		—		1,072,550		—		1,072,550
Floating Rate Notes		—		3,857,254		—		3,857,254
Repurchase Agreements		—		2,632,000		—		2,632,000
Time Deposits		—		1,006,000		—		1,006,000
Total Short-Term Investments		—		17,861,759		—		17,861,759
Total Assets	$	—	$	17,861,759	$	—	$	17,861,759

Transfers between investment levels may occur as the markets fluctuate and/or the availability of data used in an investment's valuation changes.

3.  Repurchase Agreements: The Fund may enter into repurchase agreements under which the Fund lends cash and takes possession of securities with an agreement that the counterparty will repurchase such securities. In connection with transactions in repurchase agreements, a

20

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

bank as custodian for the Fund takes possession of the underlying securities which are held as collateral, with a market value at least equal to the amount of the repurchase transaction, including principal and accrued interest. To the extent that any repurchase transaction exceeds one business day, the value of the collateral is marked-to-market on a daily basis to determine that the value of the collateral does not decrease below the repurchase price plus accrued interest as earned. If such a decrease occurs, additional collateral will be requested and, when received, will be added to the account to maintain full collateralization. In the event of default on the obligation to repurchase, the Fund has the right to liquidate the collateral and apply the proceeds in satisfaction of the obligation. In the event of default or bankruptcy by the counterparty to the agreement, realization and/or retention of the collateral or proceeds may be subject to legal proceedings. The Fund, along with other affiliated investment companies, may utilize a joint trading account for the purpose of entering into repurchase agreements.

The Fund may enter into repurchase agreements in which eligible securities are transferred into joint trading accounts maintained by the custodian for investment companies advised by the Fund's Adviser. The Fund will participate on a pro rata basis with the other investment companies in its share of the securities transferred under such repurchase agreements and in its share of proceeds from any repurchase or other disposition of such securities.

Repurchase agreements are subject to Master Repurchase Agreements which are agreements between the Fund and its counterparties that typically include provisions which provide for the net settlement of all transactions and collateral with the Fund, through a single payment, in the event of default or termination. Amounts presented on the Portfolio of Investments and Statement of Assets and Liabilities are not net settlement amounts but gross. As indicated on the Portfolio of Investments, the cash or securities to be repurchased exceeds the repurchase price to be paid under the repurchase agreement reducing the net settlement amount to zero.

4.  Indemnifications: The Trust enters into contracts that contain a variety of indemnifications. The Trust's maximum exposure under these arrangements is unknown. However, the Trust has not had prior claims or losses

pursuant to these contracts and expects the risk of loss to be remote.

5.  Dividends and Distributions to Shareholders: Dividends and distributions to shareholders are recorded on the close of each business day. Dividends from net investment income are declared daily and paid monthly. Net realized capital gains, if any, are distributed at least annually.

6.  Security Transactions, Income and Expenses: Security transactions are accounted for on the trade date (date the order to buy or sell is executed). Realized gains and losses on the sale of investment securities are determined on the specific identified cost method. Dividend income and other distributions are recorded on the ex-dividend date (except for certain foreign dividends which may be recorded as soon as the Fund is informed of such dividends) net of applicable withholding taxes. Interest income is recognized on the accrual basis except where collection is in doubt. Discounts are accreted and premiums are amortized over the life of the respective securities. Most expenses of the Trust can be directly attributed to a particular Fund. Expenses which cannot be directly attributed are apportioned among the Funds based upon relative net assets or other appropriate methods. Income, expenses (other than class specific expenses — distribution and shareholder services and transfer agency fees) and realized and unrealized gains or losses are allocated to each class of shares based upon their relative net assets.

B. Advisory Fees: The Adviser, a wholly-owned subsidiary of Morgan Stanley, provides the Fund with advisory services under the terms of an Investment Advisory Agreement, paid quarterly, at an annual rate of 0.20% of the average daily net assets of the Fund.

The Adviser has agreed to reduce its advisory fee and/or reimburse the Fund so that total annual Fund operating expenses, excluding certain investment related expenses, taxes, interest and other extraordinary expenses (including litigation), will not exceed 0.25% for Class IR shares, 0.30% for Institutional Class shares and 0.55% for Class A shares. Effective July 1, 2020, the Adviser has agreed to reduce its advisory fee and/or reimburse the Fund so that total annual Fund operating expenses will not exceed 0.45% for Class A shares. The fee waivers and/or expense reimbursements will continue for at least one year from the date of the Fund's prospectus or until

21

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

such time as the Trustees act to discontinue all or a portion of such waivers and/or reimbursements when they deem such action is appropriate. In addition, the Adviser may make additional voluntary fee waivers and/or expense reimbursements. The ratios of expenses to average net assets disclosed in the Fund's Financial Highlights may be lower than the maximum expense ratios due to these additional fee waivers and/or expense reimbursements. The Adviser may also waive additional advisory fees and/or reimburse expenses to enable the Fund to maintain a minimum level of daily net investment income. For the year ended September 30, 2020, approximately $12,455,000 of advisory fees were waived and approximately $61,000 of other expenses were reimbursed by the Adviser pursuant to this arrangement.

C. Administration Fees: The Adviser also serves as Administrator to the Trust and provides administrative services pursuant to an Administration Agreement for an annual fee, accrued daily and paid monthly, of 0.08% of the Fund's average daily net assets. Under a Sub-Administration Agreement between the Administrator and State Street Bank and Trust Company ("State Street"), State Street provides certain administrative services to the Trust. For such services, the Administrator pays State Street a portion of the fee the Administrator receives from the Fund.

D. Shareholder Services Fees: Morgan Stanley Distribution, Inc. ("MSDI" or the "Distributor"), a wholly-owned subsidiary of the Adviser, and an indirect subsidiary of Morgan Stanley, serves as the Trust's Distributor of Fund shares pursuant to a Distribution Agreement. The Trust has adopted a Shareholder Services Plan with respect to the Institutional Class shares pursuant to Rule 12b-1 under the Act. Under the Shareholder Services Plan, the Fund pays the Distributor a shareholder services fee, accrued daily and paid monthly, at an annual rate of 0.05% of the Fund's average daily net assets attributable to the Institutional Class shares.

The Trust has adopted a Shareholder Services Plan with respect to the Class A shares pursuant to Rule 12b-1 under the Act. Under the Shareholder Services Plan, the Fund pays the Distributor a shareholder services fee, accrued daily and paid monthly, at an annual rate of 0.25% of the Fund's average daily net assets attributable to the Class A shares. The Distributor has agreed to waive the 12b-1 fee on Class A shares of the Fund to the extent it exceeds 0.15% of the average daily net assets of such shares on an annualized basis. This waiver will continue for at least one year or until such time as the Trustees act to discontinue all or a portion of such waiver when it

deems such action is appropriate. For the year ended September 30, 2020, this waiver amounted to approximately $2,447,000.

The shareholder services fees are used to support the expenses associated with servicing and maintaining accounts. The Distributor may compensate other parties for providing shareholder support services to investors who purchase Institutional Class and Class A shares.

E. Dividend Disbursing and Transfer/Co-Transfer Agent: The Trust's dividend disbursing and transfer agent is DST Asset Manager Solutions, Inc. ("DST"). Pursuant to a Transfer Agency Agreement, the Trust pays DST a fee based on the number of classes, accounts and transactions relating to the Funds of the Trust.

Morgan Stanley Services Company Inc. serves as Co-Transfer Agent and provides certain transfer agency services to the Fund with respect to certain direct transactions with the Fund.

F. Custodian Fees: State Street (the "Custodian") also serves as Custodian for the Trust in accordance with a Custodian Agreement. The Custodian holds cash, securities and other assets of the Trust as required by the Act. Custody fees are payable monthly based on assets held in custody, investment purchases and sales activity and account maintenance fees, plus reimbursement for certain out-of-pocket expenses.

G. Security Transactions and Transactions with Affiliates: The Fund is permitted to purchase and sell securities ("cross-trade") from and to other Morgan Stanley funds as well as other funds and client accounts for which the Adviser or an affiliate of the Adviser serves as investment adviser, pursuant to procedures approved by the Trustees in compliance with Rule 17a-7 under the Act (the "Rule"). Each cross-trade is executed at the current market price in compliance with provisions of the Rule. For the year ended September 30, 2020, the Fund did not engage in any cross-trade transactions.

The Fund has an unfunded Deferred Compensation Plan (the "Compensation Plan"), which allows each independent Trustee to defer payment of all, or a portion, of the fees he or she receives for serving on the Board of Trustees. Each eligible Trustee generally may elect to have the deferred amounts credited with a return equal to the total return on one or more of the Morgan Stanley funds that are offered as investment options under the Compensation Plan. Appreciation/depreciation and distributions received from these investments are recorded with an offsetting increase/decrease in the deferred compensation obligation and do not affect the NAV of the Fund.

22

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

H. Federal Income Taxes: It is the Fund's intention to continue to qualify as a regulated investment company and distribute all of its taxable and tax-exempt income. Accordingly, no provision for federal income taxes is required in the financial statements.

The Fund may be subject to taxes imposed by countries in which it invests. Such taxes are generally based on income and/or capital gains earned or repatriated. Taxes are accrued based on net investment income, net realized gains and net unrealized appreciation as such income and/or gains are earned. Taxes may also be based on transactions in foreign currency and are accrued based on the value of investments denominated in such currency.

FASB ASC 740-10, "Income Taxes — Overall", sets forth a minimum threshold for financial statement recognition of the benefit of a tax position taken or expected to be taken in a tax return. Management has concluded there are no significant uncertain tax positions that would require recognition in the financial statements. If applicable, the Fund recognizes interest accrued related to unrecognized tax benefits in "Interest Expense" and penalties in "Other Expenses" in the Statement of Operations. The Fund files tax returns with the U.S. Internal Revenue Service, New York and various states. Generally, each of the tax years in the four-year period ended September 30, 2020, remains subject to examination by taxing authorities.

The tax character of distributions paid may differ from the character of distributions shown for GAAP purposes due to short-term capital gains being treated as ordinary income for tax purposes. The tax character of distributions paid during fiscal years 2020 and 2019 was as follows:

2020 Distributions Paid From: Ordinary Income (000)		2019 Distributions Paid From: Ordinary Income (000)
$	218,626	$	351,961

The amount and character of income and gains to be distributed are determined in accordance with income tax regulations which may differ from GAAP. These book/tax differences are either considered temporary or permanent in nature.

Temporary differences are attributable to differing book and tax treatments for the timing of the recognition of gains (losses) on certain investment transactions and the timing of the deductibility of certain expenses.

The Fund had no permanent differences causing reclassifications among the components of net assets for the year ended September 30, 2020.

At September 30, 2020, the components of distributable earnings for the Fund on a tax basis were as follows:

Undistributed Ordinary Income (000)		Undistributed Long-Term Capital Gain (000)
$	2,077	$	—

At September 30, 2020, the Fund had available for federal income tax purposes unused short-term capital losses of approximately $67,256,000 that do not have an expiration date.

To the extent that capital loss carryforwards are used to offset any future capital gains realized, no capital gains tax liability will be incurred by the Fund for gains realized and not distributed. To the extent that capital gains are offset, such gains will not be distributed to the shareholders.

I. Credit Facility: The Trust and other Morgan Stanley funds participated in a $300,000,000 committed, unsecured revolving line of credit facility (the "Facility") with State Street. This Facility is to be used for temporary emergency purposes or funding of shareholder redemption requests. The interest rate on borrowings is based on the federal funds rate or 1 month LIBOR rate plus a spread. The Facility also has a commitment fee of 0.25% per annum based on the unused portion of the Facility. During the year ended September 30, 2020, the Fund did not have any borrowings under the Facility.

J. Other: At September 30, 2020, the Fund had record owners of 10% or greater. Investment activities of these shareholders could have a material impact on the Fund. The aggregate percentage of such owners was 78.2%.

K. Market Risk: Certain impacts to public health conditions particular to the coronavirus (COVID-19) outbreak could impact the operations and financial performance of certain of the Fund's investments. The extent of the impact to the financial performance of the Fund's investments will depend on future developments, including (i) the duration and spread of the outbreak, (ii) the restrictions and advisories, (iii) the effects on the financial markets, and (iv) the effects on the economy overall, all of which are highly uncertain and cannot be predicted. If the financial performance of the Fund's investments

23

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

is impacted because of these factors for an extended period, the Fund's investment results may be adversely affected.

L. LIBOR Risk: The Fund's investments, payment obligations and financing terms may be based on floating rates, such as London Interbank Offer Rate ("LIBOR"), Euro Interbank Offered Rate and other similar types of reference rates (each, a "Reference Rate"). These Reference Rates are generally intended to represent the rate at which contributing banks may obtain short-term borrowings from each other within certain financial markets. On July 27, 2017, the Chief Executive of the UK Financial Conduct Authority ("FCA"), which regulates LIBOR, announced that the FCA will no longer persuade nor require banks to submit rates for the calculation of LIBOR and certain other Reference Rates after 2021. Such announcement indicates that the continuation of LIBOR and other Reference Rates on the current basis cannot and will not be guaranteed after the end of 2021. This announcement and any additional regulatory or market changes may have an adverse impact on the Fund or its investments.

In advance of 2022, regulators and market participants are currently engaged in identifying successor Reference Rates ("Alternative Reference Rates"). Additionally, prior to the end of 2021, it is expected that market participants will focus on the transition mechanisms by which the Reference Rates in existing contracts or instruments may be amended, whether through marketwide protocols, fallback contractual provisions, bespoke negotiations or amendments or otherwise. Nonetheless, the termination of certain Reference Rates presents risks to the Fund. At this time, it is not possible to completely identify or predict the effect of any such changes, any establishment of Alternative Reference Rates or any other reforms to Reference Rates that may be enacted in the UK or elsewhere. The elimination of a Reference Rate or any other changes or reforms to the determination or supervision of Reference Rates could have an adverse impact on the market for or value of any securities or payments linked to those Reference Rates and other financial obligations held by the Fund or on its overall financial condition or results of operations.

24

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Report of Independent Registered Public Accounting Firm

To the Shareholders and Board of Trustees of
Morgan Stanley Institutional Fund Trust —
Ultra-Short Income Portfolio

Opinion on the Financial Statements

We have audited the accompanying statement of assets and liabilities of Ultra-Short Income Portfolio (the "Fund") (one of the funds constituting Morgan Stanley Institutional Fund Trust (the "Trust")), including the portfolio of investments, as of September 30, 2020, and the related statement of operations for the year then ended, the statements of changes in net assets for each of the two years in the period then ended, the financial highlights for each of the four years in the period then ended and the period from April 28, 2016 (commencement of operations) through September 30, 2016 and the related notes (collectively referred to as the "financial statements"). In our opinion, the financial statements present fairly, in all material respects, the financial position of the Fund (one of the funds constituting Morgan Stanley Institutional Fund Trust) at September 30, 2020, the results of its operations for the year then ended, the changes in its net assets for each of the two years in the period then ended and its financial highlights for each of the four years in the period then ended and the period from April 28, 2016 (commencement of operations) through September 30, 2016, in conformity with U.S. generally accepted accounting principles.

Basis for Opinion

These financial statements are the responsibility of the Trust's management. Our responsibility is to express an opinion on the Fund's financial statements based on our audits. We are a public accounting firm registered with the Public Company Accounting Oversight Board (United States) ("PCAOB") and are required to be independent with respect to the Trust in accordance with the U.S. federal securities law and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB.

We conducted our audits in accordance with the standards of the PCAOB. Those standards require that we plan and perform the audit to obtain reasonable assurance about whether the financial statements are free of material misstatement, whether due to error or fraud. The Trust is not required to have, nor were we engaged to perform, an audit of the Trust's internal control over financial reporting. As part of our audits we are required to obtain an understanding of internal control over financial reporting but not for the purpose of expressing an opinion on the effectiveness of the Trust's internal control over financial reporting. Accordingly, we express no such opinion.

Our audits included performing procedures to assess the risks of material misstatement of the financial statements, whether due to error or fraud, and performing procedures that respond to those risks. Such procedures included examining, on a test basis, evidence regarding the amounts and disclosures in the financial statements. Our procedures included confirmation of securities owned as of September 30, 2020 by correspondence with the custodian and brokers or by other appropriate auditing procedures where replies from brokers were not received. Our audits also included evaluating the accounting principles used and significant estimates made by management, as well as evaluating the overall presentation of the financial statements. We believe that our audits provide a reasonable basis for our opinion.

We have served as the auditor of one or more Morgan Stanley investment companies since 2000.
Boston, Massachusetts
November 24, 2020

25

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Advisory Agreement Approval (unaudited)

Nature, Extent and Quality of Services

The Board reviewed and considered the nature and extent of the investment advisory services provided by the Adviser under the advisory agreement, including portfolio management, investment research and equity and fixed income securities trading. The Board also reviewed and considered the nature and extent of the non-advisory, administrative services provided by the Administrator under the administration agreement, including accounting, operations, clerical, bookkeeping, compliance, business management and planning, legal services and the provision of supplies, office space and utilities at the Adviser's expense. The Board also considered the Adviser's investment in personnel and infrastructure that benefits the Fund. (The Adviser and Administrator together are referred to as the "Adviser" and the advisory and administration agreements together are referred to as the "Management Agreement.") The Board also considered that the Adviser serves a variety of other investment advisory clients and has experience overseeing service providers. The Board also compared the nature of the services provided by the Adviser with similar services provided by non-affiliated advisers as prepared by Broadridge Financial Solutions, Inc. ("Broadridge").

The Board reviewed and considered the qualifications of the portfolio managers, the senior administrative managers and other key personnel of the Adviser who provide the advisory and administrative services to the Fund. The Board determined that the Adviser's portfolio managers and key personnel are well qualified by education and/or training and experience to perform the services in an efficient and professional manner. The Board concluded that the nature and extent of the advisory and administrative services provided were necessary and appropriate for the conduct of the business and investment activities of the Fund and supported its decision to approve the Management Agreement.

Performance, Fees and Expenses of the Fund

The Board reviewed the performance, fees and expenses of the Fund compared to its peers, as prepared by Broadridge, and to appropriate benchmarks where applicable. The Board discussed with the Adviser the performance goals and the actual results achieved in managing the Fund. When considering a fund's performance, the Board and the Adviser place emphasis on trends and longer-term returns (focusing on one-year, three-year and five-year performance, as of December 31, 2019, or since inception, as applicable). When a fund underperforms its benchmark and/or its peer group average, the Board and the Adviser discuss the causes of such underperformance and, where necessary, they discuss specific changes to investment strategy or investment personnel. The Board noted that the Fund's performance was better than its peer group average for the three-year period but below its peer group average for the one-year period and the period since the end of April 2016, the month of the Fund's inception. The Board discussed with the Adviser the level of the advisory and administration fees (together, the "management fee") for this Fund relative to comparable funds and/or other accounts advised by the Adviser and/or compared to its peers as prepared by Broadridge. In addition to the management fee, the Board also reviewed the Fund's total expense ratio. The Board noted that the Fund's management fee and total expense ratio were lower than its peer group averages. After discussion, the Board concluded that the Fund's (i) performance was acceptable and (ii) management fee and total expense ratio were competitive with its peer group averages.

Economies of Scale

The Board considered the size and growth prospects of the Fund and how that relates to the Fund's total expense ratio and particularly the Fund's management fee rate, which does not include breakpoints. In conjunction with its review of the Adviser's profitability, the Board discussed with the Adviser how a change in assets can affect the efficiency or effectiveness of managing the Fund and whether the management fee level is appropriate relative to current and projected asset levels and/or whether the management fee structure reflects economies of scale as asset levels change. The Board has determined that its review of the actual and/or potential economies of scale of the Fund supports its decision to approve the Management Agreement.

Profitability of the Adviser and Affiliates

The Board considered information concerning the costs incurred and profits realized by the Adviser and its affiliates during the last year from their relationship with the Fund and during the last two years from their relationship with the Morgan Stanley Fund Complex and reviewed with the Adviser the cost allocation methodology used to determine the profitability of the Adviser and affiliates. The Board has determined that its review of the analysis of the Adviser's expenses and profitability supports its decision to approve the Management Agreement.

26

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Advisory Agreement Approval (unaudited) (cont'd)

Other Benefits of the Relationship

The Board considered other direct and indirect benefits to the Adviser and/or its affiliates derived from their relationship with the Fund and other funds advised by the Adviser. These benefits may include, among other things, fees for trading, distribution and/or shareholder servicing and for transaction processing and reporting platforms used by securities lending agents, and research received by the Adviser generated from commission dollars spent on funds' portfolio trading. The Board reviewed with the Adviser these arrangements and the reasonableness of the Adviser's costs relative to the services performed. The Board has determined that its review of the other benefits received by the Adviser or its affiliates supports its decision to approve the Management Agreement.

Resources of the Adviser and Historical Relationship Between the Fund and the Adviser

The Board considered whether the Adviser is financially sound and has the resources necessary to perform its obligations under the Management Agreement. The Board also reviewed and considered the historical relationship between the Fund and the Adviser, including the organizational structure of the Adviser, the policies and procedures formulated and adopted by the Adviser for managing the Fund's operations and the Board's confidence in the competence and integrity of the senior managers and key personnel of the Adviser. The Board concluded that the Adviser has the financial resources necessary to fulfill its obligations under the Management Agreement and that it is beneficial for the Fund to continue its relationship with the Adviser.

Other Factors and Current Trends

The Board considered the controls and procedures adopted and implemented by the Adviser and monitored by the Fund's Chief Compliance Officer and concluded that the conduct of business by the Adviser indicates a good faith effort on its part to adhere to high ethical standards in the conduct of the Fund's business.

As part of the Board's review, the Board received information from management on the impact of COVID-19 on the firm generally and the Adviser and the Fund in particular including, among other information, the pandemic's current and expected impact on the Fund's performance and operations.

General Conclusion

After considering and weighing all of the above factors, with various written materials and verbal information presented by the Adviser, the Board concluded that it would be in the best interest of the Fund and its shareholders to approve renewal of the Management Agreement for another year. In reaching this conclusion the Board did not give particular weight to any single piece of information or factor referenced above. The Board considered these factors and information over the course of the year and in numerous meetings, some of which were in executive session with only the independent Board members and their counsel present. It is possible that individual Board members may have weighed these factors, and the information presented, differently in reaching their individual decisions to approve the Management Agreement.

27

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Liquidity Risk Management Program (unaudited)

In compliance with Rule 22e-4 under the Investment Company Act of 1940, as amended (the "Liquidity Rule"), the Fund has adopted and implemented a liquidity risk management program (the "Program"), which is reasonably designed to assess and manage the risk that the Fund could not meet requests to redeem shares issued by the Fund without significant dilution of remaining investors' interests in the Fund (i.e., liquidity risk). The Fund's Board of Trustees (the "Board") previously approved the designation of the Liquidity Risk Subcommittee (the "LRS") as Program administrator. The LRS is comprised of representatives from various divisions within Morgan Stanley Investment Management.

At a meeting held on April 22-23, 2020, the Board reviewed a written report prepared by the LRS that addressed the Program's operation and assessed its adequacy, and effectiveness of implementation for the period from December 1, 2018, through December 31, 2019, as required under the Liquidity Rule. The report concluded that the Program operated effectively and was adequately and effectively implemented in all material aspects, and that the relevant controls and safeguards were appropriately designed to enable the LRS to administer the Program in compliance with the Liquidity Rule.

In accordance with the Program, the LRS assessed each Fund's liquidity risk no less frequently than annually taking into consideration certain factors, as applicable, such as (i) investment strategy and liquidity of portfolio investments, (ii) short-term and long-term cash flow projections and (iii) holdings of cash and cash equivalents and borrowing arrangements and other funding sources. Certain factors are considered under both normal and reasonably foreseeable stressed conditions.

Each Fund portfolio investment is classified into one of four liquidity categories, which classification is assessed at least monthly by the LRS. The classification is based on a determination of the number of days it is reasonably expected to take to convert the investment into cash, or sell or dispose of the investment, in current market conditions without significantly changing the market value of the investment. Liquidity classification determinations take into account various market, trading and investment-specific considerations, as well as market depth, and in some cases utilize third-party vendor data.

The Liquidity Rule limits a fund's investments in illiquid investments to 15% of its net assets and requires funds that do not primarily hold assets that are highly liquid investments to determine and maintain a minimum percentage of the fund's net assets to be invested in highly liquid investments (highly liquid investment minimum or "HLIM"). The LRS believes that the Program includes provisions reasonably designed to review, monitor and comply with the 15% limit on illiquid investments and for determining, periodically reviewing and complying with the HLIM requirement, as applicable.

There can be no assurance that the Program will achieve its objectives under all circumstances in the future. Please refer to the Fund's prospectus for more information regarding the Fund's exposure to liquidity risk and other risks to which it may be subject.

28

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Privacy Notice (unaudited)  April 2019

FACTS	WHAT DOES MSIM DO WITH YOUR PERSONAL INFORMATION?
Why?	Financial companies choose how they share your personal information. Federal law gives consumers the right to limit some but not all sharing. Federal law also requires us to tell you how we collect, share, and protect your personal information. Please read this notice carefully to understand what we do.
What?	The types of personal information we collect and share depend on the product or service you have with us. This information can include: n Social Security number and income n investment experience and risk tolerance n checking account number and wire transfer instructions
How?	All financial companies need to share customers' personal information to run their everyday business. In the section below, we list the reasons financial companies can share their customers' personal information; the reasons MSIM chooses to share; and whether you can limit this sharing.

Reasons we can share your personal information	Does MSIM share?	Can you limit this sharing?
For our everyday business purposes — such as to process your transactions, maintain your account(s), respond to court orders and legal investigations, or report to credit bureaus	Yes	No
For our marketing purposes — to offer our products and services to you	Yes	No
For joint marketing with other financial companies	No	We don't share
For our affiliates' everyday business purposes — information about your transactions and experiences	Yes	No
For our affiliates' everyday business purposes — information about your creditworthiness	No	We don't share
For our affiliates to market to you	No	We don't share
For non-affiliates to market to you	No	We don't share

Questions?Call toll-free (844) 312-6327 or email: imprivacyinquiries@morganstanley.com

29

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Privacy Notice (unaudited) (cont'd)  April 2019

Who we are

Who is providing this notice? Morgan Stanley Investment Management, Inc. and its affiliated registered investment advisers, registered broker-dealers, and registered and unregistered funds ("MSIM")

What we do

How does MSIM protect my personal information?	To protect your personal information from unauthorized access and use, we use security measures that comply with federal law. These measures include computer safeguards and secured files and buildings. We have policies governing the proper handling of customer information by personnel and requiring third parties that provide support to adhere to appropriate security standards with respect to such information.
How does MSIM collect my personal information?	We collect your personal information, for example, when you n open an account or make deposits or withdrawals from your account n buy securities from us or make a wire transfer n give us your contact information We also collect your personal information from others, such as credit bureaus, affiliates, or other companies.
Why can't I limit all sharing?	Federal law gives you the right to limit only n sharing for affiliates' everyday business purposes — information about your creditworthiness n affiliates from using your information to market to you n sharing for non-affiliates to market to you State laws and individual companies may give you additional rights to limit sharing. See below for more on your rights under state law.

Definitions

Affiliates	Companies related by common ownership or control. They can be financial and non-financial companies. n Our affiliates include companies with a Morgan Stanley name and financial companies such as Morgan Stanley Smith Barney LLC and Morgan Stanley & Co.
Non-affiliates	Companies not related by common ownership or control. They can be financial and non-financial companies. n MSIM does not share with non-affiliates so they can market to you.
Joint marketing	A formal agreement between non-affiliated financial companies that together market financial products or services to you. n MSIM doesn't jointly market

Other Important Information

Vermont: Except as permitted by law, we will not share personal information we collect about Vermont residents with Non-affiliates unless you provide us with your written consent to share such information.

California: Except as permitted by law, we will not share personal information we collect about California residents with Non-affiliates and we will limit sharing such personal information with our Affiliates to comply with California privacy laws that apply to us.

30

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited)

Independent Trustees:

Name, Address and Birth Year of Independent Trustee	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years and Other Relevant Professional Experience	Number of Funds in Fund Complex Overseen by Independent Trustee**		Other Directorships Held by Independent Trustee***
Frank L. Bowman c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1944	Trustee	Since August 2006	President, Strategic Decisions, LLC (consulting) (since February 2009); Director or Trustee of various Morgan Stanley Funds (since August 2006); Chairperson of the Compliance and Insurance Committee (since October 2015); formerly, Chairperson of the Insurance Sub-Committee of the Compliance and Insurance Committee (2007-2015); served as President and Chief Executive Officer of the Nuclear Energy Institute (policy organization) (February 2005-November 2008); retired as Admiral, U.S. Navy after serving over 38 years on active duty including 8 years as Director of the Naval Nuclear Propulsion Program in the Department of the Navy and the U.S. Department of Energy (1996-2004); served as Chief of Naval Personnel (July 1994-September 1996) and on the Joint Staff as Director of Political Military Affairs (June 1992-July 1994); knighted as Honorary Knight Commander of the Most Excellent Order of the British Empire; awarded the Officier de l'Orde National du Mérite by the French Government; elected to the National Academy of Engineering (2009).		86	Director of Naval and Nuclear Technologies LLP; Director Emeritus of the Armed Services YMCA; Member of the National Security Advisory Council of the Center for U.S. Global Engagement and a member of the CNA Military Advisory Board; Trustee of Fairhaven United Methodist Church; Member of the Board of Advisors of the Dolphin Scholarship Foundation; Director of other various non-profit organizations; Formerly, Director of BP p.l.c. (November 2010-May 2019).
Kathleen A. Dennis c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1953	Trustee	Since August 2006	President, Cedarwood Associates (mutual fund and investment management consulting) (since July 2006); Chairperson of the Liquidity and Alternatives Sub-Committee of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 2006); formerly, Senior Managing Director of Victory Capital Management (1993-2006).		86	Director of various non-profit organizations.
Nancy C. Everett c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1955	Trustee	Since January 2015	Chief Executive Officer, Virginia Commonwealth University Investment Company (since November 2015); Owner, OBIR, LLC (institutional investment management consulting) (since June 2014); formerly, Managing Director, BlackRock, Inc. (February 2011-December 2013); and Chief Executive Officer, General Motors Asset Management (a/k/a Promark Global Advisors, Inc.) (June 2005-May 2010).		87	Formerly, Member of Virginia Commonwealth University School of Business Foundation (2005-2016); Member of Virginia Commonwealth University Board of Visitors (2013-2015); Member of Committee on Directors for Emerging Markets Growth Fund, Inc. (2007-2010); Chairperson of Performance Equity Management, LLC (2006-2010); and Chairperson, GMAM Absolute Return Strategies Fund, LLC (2006-2010).

31

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Address and Birth Year of Independent Trustee	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years and Other Relevant Professional Experience	Number of Funds in Fund Complex Overseen by Independent Trustee**		Other Directorships Held by Independent Trustee***
Jakki L. Haussler c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1957	Trustee	Since January 2015	Chairman, Opus Capital Group (since January 1996); formerly, Chief Executive Officer, Opus Capital Group (1996-2019); Director, Capvest Venture Fund, LP (May 2000-December 2011); Partner, Adena Ventures, LP (July 1999-December 2010); Director, The Victory Funds (February 2005-July 2008).		87	Director of Service Corporation International and Member, Audit Committee and Investment Committee; Director of Cincinnati Bell Inc. and Member, Audit Committee and Governance and Nominating Committee; Director of Northern Kentucky University Foundation and Member, Investment Committee; Member of Chase College of Law Transactional Law Practice Center Board of Advisors; Director of Chase College of Law Board of Visitors; formerly, Member, University of Cincinnati Foundation Investment Committee; Member, Miami University Board of Visitors (2008-2011); Trustee of Victory Funds (2005-2008) and Chairman, Investment Committee (2007-2008); Member, Service Provider Committee (2005-2008) and Director of Best Transport (2006-2019).
Dr. Manuel H. Johnson c/o Johnson Smick International, Inc. 220 I Street, NE — Suite 200 Washington, D.C. 20002 Birth Year 1949	Trustee	Since July 1991	Senior Partner, Johnson Smick International, Inc. (consulting firm); Chairperson of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since July 1991); Co-Chairman and a founder of the Group of Seven Council (G7C) (international economic commission); formerly, Chairperson of the Audit Committee (July 1991-September 2006), Vice Chairman of the Board of Governors of the Federal Reserve System and Assistant Secretary of the U.S. Treasury.		86	Director of NVR, Inc. (home construction).
Joseph J. Kearns c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1942	Trustee	Since August 1994	Senior Adviser, Kearns & Associates LLC (investment consulting); Chairperson of the Audit Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 1994); Director, Rubicorn Investments (since February 2019); formerly, Deputy Chairperson of the Audit Committee (July 2003-September 2006) and Chairperson of the Audit Committee of various Morgan Stanley Funds (since August 1994); CFO of the J. Paul Getty Trust (1982-1999).		87	Prior to August 10, 2016, Director of Electro Rent Corporation (equipment leasing); Prior to December 31, 2013, Director of The Ford Family Foundation.

32

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Address and Birth Year of Independent Trustee	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years and Other Relevant Professional Experience	Number of Funds in Fund Complex Overseen by Independent Trustee**		Other Directorships Held by Independent Trustee***
Michael F. Klein c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1958	Trustee	Since August 2006	Managing Director, Aetos Alternatives Management, LP (since March 2000); Co-President, Aetos Alternatives Management, LP (since January 2004) and Co-Chief Executive Officer of Aetos Alternatives Management, LP (since August 2013); Chairperson of the Fixed Income Sub-Committee of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 2006); formerly, Managing Director, Morgan Stanley & Co. Inc. and Morgan Stanley Dean Witter Investment Management and President, various Morgan Stanley Funds (June 1998-March 2000); Principal, Morgan Stanley & Co. Inc. and Morgan Stanley Dean Witter Investment Management (August 1997-December 1999).		86	Director of certain investment funds managed or sponsored by Aetos Alternatives Management, LP; Director of Sanitized AG and Sanitized Marketing AG (specialty chemicals).
Patricia Maleski c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1960	Trustee	Since January 2017	Managing Director, JPMorgan Asset Management (2004-2016); Oversight and Control Head of Fiduciary and Conflicts of Interest Program (2015-2016); Chief Control Officer-Global Asset Management (2013-2015); President, JPMorgan Funds (2010-2013); Chief Administrative Officer (2004-2013); various other positions including Treasurer and Board Liaison (since 2001).		87	None.
W. Allen Reed c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1947	Chair of the Board and Trustee	Chair of the Boards since August 2020 and Trustee since August 2006	Chair of the Boards of various Morgan Stanley Funds (since August 2020); Chairperson of the Governance Committee; Chairperson of the Equity Sub-Committee of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 2006); formerly, Vice Chair of the Boards of various Morgan Stanley Funds (January 2020-August 2020); President and Chief Executive Officer of General Motors Asset Management; Chairman and Chief Executive Officer of the GM Trust Bank and Corporate Vice President of General Motors Corporation (August 1994-December 2005).		86	Formerly, Director of Legg Mason, Inc. (2006-2019); and Director of the Auburn University Foundation (2010-2015).

*  This is the earliest date the Trustee began serving the Morgan Stanley Funds. Each Trustee serves an indefinite term, until his or her successor is elected.

**  The Fund Complex includes (as of December 31, 2019) all open-end and closed-end funds (including all of their portfolios) advised by Morgan Stanley Investment Management Inc. (the "Adviser") and any funds that have an adviser that is an affiliated person of the Adviser (including, but not limited to, Morgan Stanley AIP GP LP).

***  This includes any directorships at public companies and registered investment companies held by the Trustee at any time during the past five years.

33

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited) (cont'd)

Executive Officers:

Name, Address and Birth Year of Executive Officer	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years
John H. Gernon 522 Fifth Avenue New York, NY 10036 Birth Year 1963	President and Principal Executive Officer	Since September 2013	President and Principal Executive Officer of the Equity and Fixed Income Funds and the Morgan Stanley AIP Funds (since September 2013) and the Liquidity Funds and various money market funds (since May 2014) in the Fund Complex; Managing Director of the Adviser; Head of Public Markets Product Development (since 2006).
Timothy J. Knierim 522 Fifth Avenue New York, NY 10036 Birth Year 1959	Chief Compliance Officer	Since December 2016	Managing Director of the Adviser and various entities affiliated with the Adviser; Chief Compliance Officer of various Morgan Stanley Funds and the Adviser (since December 2016) and Chief Compliance Officer of Morgan Stanley AIP GP LP (since 2014). Formerly, Managing Director and Deputy Chief Compliance Officer of the Adviser (2014-2016); and formerly, Chief Compliance Officer of Prudential Investment Management, Inc. (2007-2014).
Francis J. Smith 522 Fifth Avenue New York, NY 10036 Birth Year 1965	Treasurer and Principal Financial Officer	Treasurer since July 2003 and Principal Financial Officer since September 2002	Managing Director of the Adviser and various entities affiliated with the Adviser; Treasurer (since July 2003) and Principal Financial Officer of various Morgan Stanley Funds (since September 2002).
Mary E. Mullin 522 Fifth Avenue New York, NY 10036 Birth Year 1967	Secretary	Since June 1999	Managing Director of the Adviser; Secretary of various Morgan Stanley Funds (since June 1999).
Michael J. Key 522 Fifth Avenue New York, NY 10036 Birth Year 1979	Vice President	Since June 2017	Vice President of the Equity and Fixed Income Funds, Liquidity Funds, various money market funds and the Morgan Stanley AIP Funds in the Fund Complex (since June 2017); Executive Director of the Adviser; Head of Product Development for Equity and Fixed Income Funds (since August 2013).

*  This is the earliest date the officer began serving the Morgan Stanley Funds. Each officer serves a one-year term, until his or her successor is elected and qualifies.

34

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Adviser and Administrator

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

Distributor

Morgan Stanley Distribution, Inc.
522 Fifth Avenue
New York, New York 10036

Dividend Disbursing and Transfer Agent

DST Asset Manager Solutions, Inc.
2000 Crown Colony Drive
Quincy, Massachusetts 02169

Co-Transfer Agent

Morgan Stanley Services Company, Inc.
522 Fifth Avenue
New York, New York 10036

Custodian

State Street Bank and Trust Company
One Lincoln Street
Boston, Massachusetts 02111

Legal Counsel

Dechert LLP
1095 Avenue of the Americas
New York, New York 10036

Counsel to the Independent Trustees

Perkins Coie LLP
1155 Avenue of the Americas,
22nd Floor
New York, New York 10036

Independent Registered Public Accounting Firm

Ernst & Young LLP
200 Clarendon Street
Boston, Massachusetts 02116

Reporting to Shareholders

Each Morgan Stanley fund provides a complete schedule of portfolio holdings in its Semi-Annual and the Annual Reports within 60 days of the end of the fund's second and fourth fiscal quarters. The Semi-Annual and Annual Reports are filed electronically with the Securities and Exchange Commission ("SEC") on Form N-CSRS and Form N-CSR, respectively. Morgan Stanley also delivers the Semi-Annual and Annual Reports to fund shareholders and makes these reports available on its public website, www.morganstanley.com/im/shareholderreports. Each Morgan Stanley non-money market fund also files a complete schedule of portfolio holdings with the SEC for the fund's first and third fiscal quarters as an attachment to Form N-PORT. Morgan Stanley does not deliver the reports for the first and third fiscal quarters to shareholders, nor are the reports posted to the Morgan Stanley public website. However, the holdings for each money market fund are posted to the Morgan Stanley public website. You may obtain the Form N-PORT filings (as well as the Form N-CSR and N-CSRS filings) by accessing the SEC's website, www.sec.gov. You can also request copies of these materials, upon payment of a duplicating fee, by electronic request at the SEC's email address (publicinfo@sec.gov).

Proxy Voting Policies and Procedures and Proxy Voting Record

You may obtain a copy of the Trust's Proxy Voting Policy and Procedures and information regarding how the Trust voted proxies relating to portfolio securities during the most recent twelve-month period ended June 30, without charge, upon request, by calling toll free 1 (800) 548-7786 or by visiting our website at www.morganstanley.com/im/shareholderreports. This information is also available on the SEC's website at www.sec.gov.

This report is authorized for distribution only when preceded or accompanied by a prospectus or summary prospectus of the applicable Fund of Morgan Stanley Institutional Fund Trust, which describes in detail the Fund's investment policies, risks, fees and expenses. Please read the prospectus carefully before you invest or send money. For additional information, including information regarding the investments comprising the Fund, please visit our website at www.morganstanley.com/im/shareholderreports or call toll free 1 (800) 548-7786.

35

Printed in U.S.A.
This Report has been prepared for shareholders and may be distributed to others only if preceded or accompanied by a current prospectus.

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

© 2020 Morgan Stanley. Morgan Stanley Distribution, Inc.

IFTUSIANN
3299158 EXP 11.30.21

INVESTMENT MANAGEMENT

Morgan Stanley Institutional Fund Trust

Ultra-Short Municipal Income Portfolio

Annual Report

September 30, 2020

Beginning on January 1, 2021, as permitted by regulations adopted by the Securities and Exchange Commission ("SEC"), paper copies of the Fund's Annual and Semi-Annual Reports to Shareholders ("Shareholder Reports") will no longer be sent by mail, unless you specifically request paper copies of the Shareholder Reports from the Fund or from your financial intermediary, such as a broker-dealer or a bank. Instead, the Shareholder Reports will be made available on the Fund's website, https://www.morganstanley.com/im/shareholderreports and you will be notified by mail each time a Shareholder Report is posted and provided with a website link to access the Shareholder Report. If you already elected to receive Shareholder Reports electronically, you will not be affected by this change and you need not take any action. You may elect to receive Shareholder Reports and other communications from the Fund electronically anytime by contacting your financial intermediary or, if you are a direct investor, please follow the instructions on the envelope.

Beginning on January 1, 2019, you may elect to receive all future Shareholder Reports in paper free of charge. If you invest through a financial intermediary, you can contact your financial intermediary to request that you continue to receive paper copies of your Shareholder Reports. If you invest directly with the Fund, please follow the instructions on the envelope to let the Fund know you wish to continue receiving paper copies of your Shareholder Reports. Your election to receive Shareholder Reports in paper will apply to all funds held in your account if you invest through your financial intermediary or all funds held with the fund complex if you invest directly with a fund.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Table of Contents

Shareholders' Letter	2
Expense Example	3
Investment Overview	4
Portfolio of Investments	7
Statement of Assets and Liabilities	10
Statement of Operations	11
Statements of Changes in Net Assets	12
Financial Highlights	13
Notes to Financial Statements	16
Report of Independent Registered Public Accounting Firm	21
Investment Advisory Agreement Approval	22
Liquidity Risk Management Program	24
Federal Tax Notice	25
Privacy Notice	26
Trustee and Officer Information	28

This report is authorized for distribution only when preceded or accompanied by a prospectus or summary prospectus of the applicable Fund of the Morgan Stanley Institutional Fund Trust. To receive a prospectus and/or statement of additional information ("SAI"), which contains more complete information such as investment objectives, charges, expenses, policies for voting proxies, risk considerations and describes in detail each of the Fund's investment policies to the prospective investor, please call toll free 1 (800) 548-7786. Please read the prospectuses carefully before you invest or send money.

Additionally, you can access information about the Fund, including performance, characteristics and investment team commentary, through Morgan Stanley Investment Management's website: www.morganstanley.com/im/shareholderreports.

Market forecasts provided in this report may not necessarily come to pass. There is no guarantee that any sectors mentioned will continue to perform as discussed herein or that securities in such sectors will be held by the Fund in the future. There is no assurance that a fund will achieve its investment objective. Funds are subject to market risk, which is the possibility that market values of securities owned by the Fund will decline and, therefore, the value of the Fund's shares may be less than what you paid for them. Accordingly, you can lose money investing in this Fund. Please see the prospectus for more complete information on investment risks.

1

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Shareholders' Letter (unaudited)

Dear Shareholders,

We are pleased to provide this Annual Report, in which you will learn how your investment in Ultra-Short Municipal Income Portfolio (the "Fund") performed during the latest twelve-month period.

Morgan Stanley Investment Management is a client-centric, investor-led organization. Our global presence, intellectual capital, and breadth of products and services enable us to partner with investors to meet the evolving challenges of today's financial markets. We aim to deliver superior investment service and to empower our clients to make the informed decisions that help them reach their investment goals.

As always, we thank you for selecting Morgan Stanley Investment Management, and look forward to working with you in the months and years ahead.

Sincerely,

John H. Gernon
President and Principal Executive Officer

October 2020

2

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Expense Example (unaudited)

Ultra-Short Municipal Income Portfolio

As a shareholder of the Fund, you may incur two types of costs: (1) transactional costs; and (2) ongoing costs, which may include advisory fees, administration fees, distribution and shareholder services fees; and other Fund expenses. This example is intended to help you understand your ongoing costs (in dollars) of investing in the Fund and to compare these costs with the ongoing costs of investing in other mutual funds.

This example is based on an investment of $1,000 invested at the beginning of the six-month period ended September 30, 2020 and held for the entire six-month period.

Actual Expenses

The table below provides information about actual account values and actual expenses. You may use the information in this table, together with the amount you invested, to estimate the expenses that you paid over the period. Simply divide your account value by $1,000 (for example, an $8,600 account value divided by $1,000 = 8.6), then multiply the result by the number in the table under the heading entitled "Actual Expenses Paid During Period" to estimate the expenses you paid on your account during this period.

Hypothetical Example for Comparison Purposes

The table below provides information about hypothetical account values and hypothetical expenses based on the Fund's actual expense ratio and an assumed rate of return of 5% per year before expenses, which is not the Fund's actual return. The hypothetical account values and expenses may not be used to estimate the actual ending account balance or expenses you paid for the period. You may use this information to compare the ongoing costs of investing in the Fund and other funds. To do so, compare this 5% hypothetical example with the 5% hypothetical examples that appear in the shareholder reports of the other funds.

Please note that the expenses shown in the table are meant to highlight your ongoing costs only and do not reflect any transactional costs. Therefore, the information for each class in the table is useful in comparing ongoing costs only, and will not help you determine the relative total costs of owning different funds. In addition, if these transactional costs were included, your costs would have been higher.

	Beginning Account Value 4/1/20		Actual Ending Account Value 9/30/20		Hypothetical Ending Account Value		Actual Expenses Paid During Period*		Hypothetical Expenses Paid During Period*		Net Expense Ratio During Period**
Ultra-Short Municipal Income Portfolio Class IR	$	1,000.00	$	1,002.20	$	1,024.35	$	0.65	$	0.66		0.13	%
Ultra-Short Municipal Income Portfolio Institutional Class		1,000.00		1,002.70		1,023.85		1.15		1.16		0.23
Ultra-Short Municipal Income Portfolio Class A		1,000.00		1,001.30		1,023.50		1.50		1.52		0.30

*  Expenses are calculated using each Fund Class' annualized net expense ratio (as disclosed), multiplied by the average account value over the period and multiplied by 183/366 (to reflect the most recent one-half year period).

**  Annualized.

3

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Overview (unaudited)

Ultra-Short Municipal Income Portfolio

The Fund seeks current income exempt from federal income tax and capital preservation while maintaining liquidity.

Performance

For the fiscal year ended September 30, 2020, the Fund's Institutional Class Share had a total return based on net asset value and reinvestment of distributions per share of 1.01%, net of fees. The Fund's Institutional Class Share outperformed against the Fund's benchmark, the Bloomberg BVAL Municipal AAA Yield Curve (Callable) 3 Month Index (the "Index"), which returned 0.64%. For the seven-day period ended September 30, 2020, the Fund's Institutional Class Share provided an annualized current yield of 0.06% (subsidized) and –0.30% (non-subsidized), while its 30-day moving average annualized yield was 0.04% (subsidized) and –0.32% (non-subsidized). The 30-day SEC yield was 0.04% (subsidized) and –0.32% (non-subsidized). The 30-day taxable equivalent SEC yield was 0.06% (subsidized) and –0.50% (non-subsidized). The non-subsidized yield reflects what the yield would have been had a fee and/or expense waiver not been in place during the period shown. Past performance is no guarantee of future results.

Factors Affecting Performance

•  Municipal bonds experienced significant volatility in the first half of 2020 triggered by the global pandemic. The increase in short-term tax-exempt yields in March 2020 was largely a supply and demand situation related to redemption activity across the money market fund industry. The Securities Industry and Financial Markets Association (SIFMA) Municipal Swap Index, which is a 7-day high-grade market index comprised of tax-exempt variable rate demand obligations (VRDOs), spiked to a high of 5.20% on March 18, 2020.ⁱ

•  As fund flows stabilized across money markets and supply in tax-exempt securities became limited, yields dropped from the March highs. At the same time, the Federal Reserve (Fed) and central banks around the world injected liquidity into the short-term markets. To combat the economic slowdown from the prolonged shutdown, the Fed announced that it would extend asset purchases (known as quantitative easing) to support the economy to an unlimited amount, as well as include other assets such as corporate and municipal bonds. In addition, the Fed created the Money Market Liquidity

  Facility to support prime and tax-exempt money markets. Importantly, the concerns in the overall money market industry were largely unrelated to tax-exempt/municipal securities; this was a liquidity crisis.

•  On April 9, 2020, the Fed announced the creation of the Municipal Liquidity Facility (MLF) to help state and local governments better manage cash flow pressures to continue to serve households and businesses in their communities. With the creation of the MLF, the broader municipal market stabilized and began to normalize through May 2020.

•  After a strong three-month recovery, the muni market began to cool in the later part of the third quarter of 2020. All-time low yields, uncertainty around additional fiscal support and less favorable supply-demand dynamics began to weigh on the market.

•  Issuance remained high through the third quarter of 2020 (at $47.28 billion for the month of September, the highest monthly issuance since records began in 1986).ⁱⁱ Supply continued to outpace reinvestment of income from coupons, calls and maturities, negating the net negative supply that typically occurs at this time of year. Bid-wanted activity increased in the secondary market, while dealer inventories remained near multi-year lows, signaling a weaker appetite for municipal bonds among the broker-dealer community.

•  Investor flows into municipal bond funds remained net positive but waned later in the third quarter of 2020 as valuations became stretched and fundamental concerns resurfaced. The inability of Congress to reach an agreement on another round of fiscal aid was causing concerns that cities and states will be ill-equipped to address an estimated $1 trillion of budgetary shortfalls.ⁱⁱⁱ However, we note that most municipal issuers have ample capacity to meet their obligations without federal assistance.

ⁱ  Source: Bloomberg L.P. The SIFMA Index is issued weekly and is compiled from the weekly interest rate resets of tax-exempt variable rate issues included in a database maintained by Municipal Market Data which meet specific criteria established from time to time by the Securities Industry and Financial Markets Association. The index performance is provided for illustrative purposes only and is not meant to depict the performance of a specific investment.

ⁱⁱ  Source: The Bond Buyer, September 30, 2020.

ⁱⁱⁱ  Source: Barron's, "Cities and States are Facing a $1 Trillion Budget Mess. There Will Be More Trouble Ahead," Leslie P. Norton and Stephen Kleege, August 28, 2020.

4

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Overview (unaudited) (cont'd)

Ultra-Short Municipal Income Portfolio

•  While state and local governments will face significant headwinds as they finalize their 2021 and 2022 budgets, state governments have broad powers to recover lost revenues and cut spending to balance their budgets. Most municipal governments are highly rated and have the constitutional ability to incur debt until revenues recover. Issuance has spiked in recent months as borrowers take advantage of low rates to reduce their interest expense. Large lower-quality borrowers have tapped into the Fed's Municipal Liquidity Facility to cover operating costs at lower rates than those available in the traditional municipal bond market.

•  Key positive contributors to the Fund's performance included its high exposure to floating- and variable-rate notes (63% of the portfolio as of September 30, 2020). The Fund's floating-rate note (FRN) holdings benefited from relatively low price volatility in the period, and the Fund captured strong income from FRN holdings.

•  The Fund's sector and credit quality allocations were favorable to performance as credit rebounded in May and June 2020 after the sell-off in March 2020. The Fund's overweight allocation in corporate credit (industrial development revenue/pollution control revenue bonds), utility bonds and health care bonds outperformed as these sectors recovered.

•  However, the declining interest rate environment has limited reinvestment opportunities, as coupon income and the proceeds from called and maturing bonds are reinvested into the lower yielding bonds on offer in the current market. Additionally, market technicals were a headwind to performance later in the period. Strong issuance in the third quarter of 2020 led to the refunding and call of many FRN holdings.

Management Strategies

•  We anticipate increased volatility in the months ahead and a less favorable supply and demand dynamic that will likely act as a near-term drag on the market. We believe that clarity around the size and scope of additional federal stimulus is necessary to mitigate uncertainty and ease investor concerns.

•  We maintain a short duration stance given stretched valuations and the potential for increased volatility in the coming months. We continue to hold a bias toward higher quality assets overall and continue to advocate careful security selection as the impact of the pandemic varies across market segments. We prefer essential service revenue issues such as water & sewer, public power and pollution control. With the front end of the municipal yield curve being flat, we believe the portfolio can continue to benefit in terms of liquidity and income. The Fund's exposures to variable-rate demand notes, FRNs and 3-month put and tender option bond rolls may contribute to higher income and principal stability, as well as provide the flexibility to adjust and take advantage of market opportunities as they present.

5

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Overview (unaudited) (cont'd)

Ultra-Short Municipal Income Portfolio

*  Minimum Investment

**  Commenced operations on December 19, 2018.

In accordance with SEC regulations, the Fund's performance shown assumes that all recurring fees (including management fees) were deducted and all dividends and distributions were reinvested. The performance of Class A and Class IR shares will vary from the performance of Institutional Class shares and will be negatively impacted by additional fees assessed to those classes (where applicable).

Performance Compared to the Bloomberg BVAL Municipal AAA Yield Curve (Callable) 3 Month Index⁽¹⁾, and the Lipper Short Municipal Debt Funds Index⁽²⁾

	Period Ended September 30, 2020 Total Returns(3)
				Average Annual
	One Year			Five Years		Ten Years		Since Inception(5)
Fund — Class IR Shares w/o sales charges(4)		0.91	%		—		—		1.18	%
Fund — Institutional Class Shares w/o sales charges(4)		1.01			—		—		1.20
Fund — Class A Shares w/o sales charges(4)		0.73			—		—		0.99
Bloomberg BVAL Municipal AAA Yield Curve (Callable) 3 Month Index		0.64			—		—		0.94
Lipper Short Municipal Debt Funds Index		1.80			—		—		2.24

Performance data quoted represents past performance, which is no guarantee of future results, and current performance may be lower or higher than the figures shown. Performance assumes that all dividends and distributions, if any, were reinvested. For the most recent month-end performance figures, please visit www.morganstanley.com/im/shareholderreports. Investment returns and principal value will fluctuate so that Fund shares, when redeemed, may be worth more or less than their original cost. Total returns do not reflect the deduction of taxes that a shareholder would pay on Fund distributions or the redemption of Fund shares. Performance of share classes will vary due to differences in expenses.

⁽¹⁾  Bloomberg BVAL Municipal AAA Yield Curve (Callable) 3 Month Index is Bloomberg's evaluated pricing service, BVAL, provides a municipal "AAA" 5% coupon benchmark yield curve that is the baseline curve for BVAL tax-exempt municipals. It is populated with high quality U.S. municipal bonds with an average rating of "AAA" from Moody's and S&P. The yield curve is built using non-parametric fit of market data obtained from the Municipal Securities Rulemaking Board, new issues and other proprietary contributed prices. The benchmark is updated hourly and utilizes eligible "AAA" traded observations throughout the day and accessible on through Bloomberg services. The Index is unmanaged and its returns do not include any sales charges or fees. Such costs would lower performance. It is not possible to invest directly in an index.

⁽²⁾  The Lipper Short Municipal Debt Funds Index is an equally weighted performance index of the largest qualifying funds (based on net assets) in the Lipper Short Municipal Debt Funds classification. The Index, which is adjusted for capital gains distributions and income dividends, is unmanaged and should not be considered an investment. There are currently 30 funds represented in this Index. As of the date of this report, the Fund was in the Lipper Short Municipal Debt Funds classification.

⁽³⁾  Total returns for the Fund reflect expenses waived and/or reimbursed, if applicable, by the Adviser. Without such waivers and/or reimbursements, total returns would have been lower.

⁽⁴⁾  Commenced operations on December 19, 2018.

⁽⁵⁾  For comparative purposes, average annual since inception returns listed for the Indexes refer to the inception date of the Fund, not the inception of the Indexes.

6

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments

Ultra-Short Municipal Income Portfolio

	Face Amount (000)		Value (000)
Weekly Variable Rate Bonds (a) (29.2%)
Ascension Parish, LA, BASF Corp. Project Ser 1995 (AMT) 0.30%, 3/1/25	$	2,400	$	2,400
Blytheville Arkansas Industrial, AR, Development Revenue Variable Refunding Revenue Bonds Nucor Corp. 2002 0.20%, 1/2/33		8,000		8,000
Brazos, TX, River Harbor Navigation District BASF Corp. Project Ser 1996 (AMT)
0.30%, 4/1/31		5,000		5,000
Iowa State Finance Authority, Midwestern Disaster Area Revenue Bonds Archer-Daniels-Midland Company Project Series 2012
0.16%, 12/1/45		10,000		10,000
Solid Waste Facilities Revenue Bonds, Mid America Energy Company Project, Ser 2016 B (AMT)
0.19%, 12/1/46		7,500		7,500
Solid Waste Facilities Revenue Bonds, Mid America Energy Company Project, Ser 2017
0.17%, 12/1/47		7,500		7,500
Kentucky Economic Development Finance Authority, KY, Catholic Health Initiatives Ser 2004 C
0.21%, 5/1/34		2,400		2,400
Mississippi Business Finance Corporation, MS, Solid Waste Disposal Revenue Variable Bonds Waste Management Inc 2003
0.18%, 7/1/28		3,500		3,500
Parish of St. James, State of Louisiana Revenue Bonds, LA, Nucor Steel Louisiana LLC Project, Series 2010B-1, Gulf Opportunity Zone Bonds
0.20%, 11/1/40		1,500		1,500
Port Arthur, TX, Navigation District Revenue Multi-Modal Variable Rate Demand Revenue Bonds BASF Corp. 1998
0.30%, 4/1/33		7,600		7,600
RBC Municipal Products Trust, Inc., NA, Various States Certificates E-141
0.15%, 12/1/23 (b)		4,000		4,000
Various States Certificates E-145
0.15%, 9/8/21 (b)		4,000		4,000
RBC Municipal Products Trust, Inc., MA, Partners Healthcare System Adjustable Ser 2019 T-2 Floater Certificates Ser 2018-E-130
0.15%, 11/1/23 (b)		1,000		1,000
RBC Municipal Products Trust, Inc., MO, Health and Educational Facilities Authority of the State of Missouri SSM Health Ser 2019 A Floater Certificates Ser 2019-C17
0.17%, 12/1/39 (b)		2,000		2,000

	Face Amount (000)		Value (000)
RBC Municipal Products Trust, Inc., NY, New York City Variable Ser 2006 Subser I-5 Floater Certificates Ser 2019-E133
0.15%, 5/1/23 (b)	$	4,000	$	4,000
Tender Option Bond Trust, TX, Harris County Cultural Education Facilities Financing Corporation Baylor College of Medicine Ser B Puttable Floating Rate Receipts Ser 2019-BAML 5012
0.17%, 11/15/46 (b)		4,255		4,255
Utah Water Finance Agency, Ser 2008 B
0.15%, 10/1/37		2,065		2,065
Washington County, Nebraska Industrial Development Revenue Bonds (Cargill, Inc. Recovery Zone Facility Project) Series 2010B
0.15%, 12/1/40		15,000		15,000
Total Weekly Variable Rate Bonds (Cost $91,720)				91,720
Daily Variable Rate Bonds (a) (21.6%)
Bay County, Florida Industrial Development Revenue Bonds (Gulf Power Company Project), Series 2020
0.17%, 6/1/50		15,000		15,000
Harris County Cultural Education Facilities Finance Corporation Revenue Bonds, TX, Houston Methodist Series 2020B
0.14%, 12/1/59		4,000		4,000
Indiana Finance Authority, Environmental Refunding Duke Energy Indiana Inc Ser 2009 A-4
0.13%, 12/1/39		5,000		5,000
JP Morgan Chase Putters, NA, Drivers Trust Various States Certificates 5032
0.15%, 12/15/34 (b)		15,000		15,000
Drivers Trust Various States Certificates 5033
0.34%, 2/16/22 (b)		1,000		1,000
Drivers Trust Various States Certificates 5035
0.15%, 2/1/21 (b)		5,000		5,000
Louisville and Jefferson County, KY, Regional Airport UPS Worldwide
0.15%, 1/1/29		8,000		8,000
The Industrial Development Board of The Town of Columbia Pollution Control Revenue Refunding Bonds, AL, Alabama Power Company Project Series 2014-C
0.15%, 12/1/37		5,000		5,000
West Jefferson, AL, Industrial Development Board Solid Waste Disposal Revenue Alabama Power- Miller Plant Ser 2008 (AMT)
0.17%, 12/1/38		10,000		10,000
Total Daily Variable Rate Bonds (Cost $68,000)				68,000
Closed-End Investment Companies (a) (9.8%)
BlackRock MuniYield Investment Fund, Inc. (MYF), OT, VRDP Ser W-7-594 (AMT)
0.22%, 6/1/41 (b)		4,000		4,000
BlackRock MuniYield Quality Fund III, Inc. (MYI), OT, VRDP (AMT)
0.22%, 6/1/41 (b)		2,400		2,400

The accompanying notes are an integral part of the financial statements.
7

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Ultra-Short Municipal Income Portfolio

	Face Amount (000)		Value (000)
Closed-End Investment Companies (a) (cont'd)
JP Morgan Chase & Co., OT, Variable Rate Muni Term Preferred- Invesco Value Municipal Income Trust PUTTERs Ser 5027 (AMT)
0.34%, 6/1/21 (b)	$	10,000	$	10,000
Nuveen AMT-Free Municipal Credit Income Fund, MFP Share Ser B
0.68%, 3/1/29 (b)		5,000		5,000
Nuveen New York AMT Free Quality Municipal Income Fund 800, Ser E (AMT)
1.70%, 5/1/47 (b)		5,000		5,000
Nuveen Quality Municipal Income Fund, Ser 2-2525 (AMT)
1.46%, 9/11/26 (b)		2,400		2,400
Western Asset Managed Municipals Fund Inc, OT, VRDP Ser 1 (AMT)
0.20%, 3/4/45 (b)		2,000		2,000
Total Closed-End Investment Companies (Cost $30,800)				30,800
Floating Rate Notes (a) (12.7%)
Colorado Health Facilities Authority Revenue Bonds, CO, Series 2008C-2
1.36%, 10/1/39		300		300
Indiana Finance Authority Economic Development Refunding Revenue Bonds, IN, Republic Services, Inc. Project Series 2010A (AMT)
0.28%, 5/1/34		9,500		9,507
Metropolitan Water District of Southern California, Water Ser 2017 E
0.37%, 7/1/37		4,500		4,502
Michigan Finance Authority Hospital Refunding Bonds McLaren Health Care Ser 2015D-2
0.62%, 10/15/38		7,500		7,501
Michigan State Finance Authority, Trinity Health Credit Group Ser 2015
0.64%, 12/1/39		6,010		6,009
New York City Cultural Resources Trust, NY, American Museum of Natural History Ser 2014 B1
0.32%, 4/1/44		5,000		5,000
Public Finance Authority Solid Waste Disposal Refunding Revenue Bonds, WI, Waste Management, Inc. Project Series 2017A-2
0.45%, 10/1/25		7,000		7,000
Total Floating Rate Notes (Cost $39,810)				39,819
Quarterly Variable Rate Bonds (a) (3.4%)
Miami-Dade County, FL, Industrial Development Authority Solid Waste Management, Inc. of Florida Ser 2011 (AMT)
1.60%, 11/1/41		4,500		4,505
Pennsylvania Economic Development Financing Authority, Republic Service, Inc. Ser 2019A (AMT)
0.60%, 4/1/34		1,100		1,100
The Industrial Development Authority of The City of Phoenix, AZ, Solid Waste Disposal Revenue Refunding Bonds Series 2013
0.48%, 12/1/35		5,000		5,001
Total Quarterly Variable Rate Bonds (Cost $10,600)				10,606

	Face Amount (000)		Value (000)
Semi-Annual Variable Rate Bonds (a) (3.6%)
RBC Municipal Products Trust, Inc., CO, City and County of Denver, Airport System — Subordinate Bonds Floater Certificates Ser 2019-G114
0.37%, 12/1/26 (b)	$	6,000	$	6,000
RBC Municipal Products Trust, Inc., FL, Broward County Port Facilities Revenue Ser B Floater Certificates Ser 2019-G115
0.37%, 9/1/27 (b)		4,000		4,000
RBC Municipal Products Trust, Inc., SC, Transportation Infrastructure Bank Ser 2017 A, Floater Certificates Ser 2019-G109
0.32%, 10/1/25 (b)		1,500		1,500
Total Semi-Annual Variable Rate Bond (Cost $11,500)				11,500
Commercial Paper (c) (14.3%)
JEA FLA Electric System Revenue, FL, Commercial Paper 3/A2 Sub Ser 2000-F-2
0.20%, 10/1/20		4,000		4,000
0.28%, 10/9/20		11,000		11,000
Mercer County, ND, Pollution Control Commercial Paper Notes 3/A2 Ser 1
0.20%, 10/2/20		3,000		3,000
0.21%, 10/8/20		12,000		12,000
York County, SC, National Rural Utilities Cooperative Finance Corporation Pollution Control Revenue IAM Commercial Paper 3/A2 Ser 2000
0.18%, 10/1/20		15,000		15,000
Total Commercial Paper (Cost $45,000)				45,000
Municipal Bonds & Notes (6.2%)
Dormitory Authority of The State of New York State Personal Income Tax Subordinate RANs, Ser 2020 B
5.00%, 3/31/21		2,900		2,970
Miami-Dade County, FL, Aviation Revenue Miami International Airport Series 2012 A (AMT)
5.00%, 10/1/20		1,950		1,950
State of Texas Tax And Revenue Anticipation Notes, Series 2020 (TX)
4.00%, 8/26/21		14,000		14,481
Total Municipal Bonds & Notes (Cost $19,389)				19,401
Total Investments (100.8%) (Cost $316,819) (d)				316,846
Liabilities in Excess of Other Assets (–0.8%)				(2,648	)
Net Assets (100.0%)			$	314,198

(a)  Floating or variable rate securities: The rates disclosed are as of September 30, 2020. For securities based on a published reference rate and spread, the reference rate and spread are indicated in the description in the Portfolio of Investments. Certain variable rate securities may not be based on a published reference rate and spread but are determined by the issuer or agent and are based on current market conditions. These securities do not indicate a reference rate and spread in their description in the Portfolio of Investments.

(b)  144A security — Certain conditions for public sale may exist. Unless otherwise noted, these securities are deemed to be liquid.

The accompanying notes are an integral part of the financial statements.
8

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Portfolio of Investments (cont'd)

Ultra-Short Municipal Income Portfolio

(c)  The rates shown are the effective yields at the date of purchase.

(d)  At September 30, 2020, the aggregate cost for federal income tax purposes is approximately $316,819,000. The aggregate gross unrealized appreciation is approximately $28,000 and the aggregate gross unrealized depreciation is approximately $1,000, resulting in net unrealized appreciation of approximately $27,000.

AMT  Alternative Minimum Tax.

PUTTERs  Puttable Tax-Exempt Receipts.

RANs  Revenue Anticipation Notes.

VRDP  Variable Rate Demand Preferred.

Portfolio Composition

Classification	Percentage of Total Investments
Weekly Variable Rate Bonds		28.9	%
Daily Variable Rate Bonds		21.5
Commercial Paper		14.2
Floating Rate Notes		12.6
Closed-End Investment Companies		9.7
Other*		7.0
Municipal Bonds & Notes		6.1
Total Investments		100.0	%

*  Industries and/or investment types representing less than 5% of total investments.

The accompanying notes are an integral part of the financial statements.
9

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Ultra-Short Municipal Income Portfolio

Statement of Assets and Liabilities	September 30, 2020 (000)
Assets:
Investments in Securities of Unaffiliated Issuers, at Value (Cost $316,819)	$	316,846
Cash		120
Receivable for Fund Shares Sold		645
Interest Receivable		243
Due from Adviser		85
Receivable for Investments Sold		80
Other Assets		47
Total Assets		318,066
Liabilities:
Payable for Fund Shares Redeemed		3,760
Payable for Professional Fees		45
Payable for Shareholder Services Fees — Institutional Class		1
Payable for Shareholder Services Fees — Class A		24
Payable for Administration Fees		21
Payable for Custodian Fees		3
Payable for Transfer Agency Fees — Class IR		—	@
Payable for Transfer Agency Fees — Institutional Class		1
Payable for Transfer Agency Fees — Class A		1
Other Liabilities		12
Total Liabilities		3,868
Net Assets	$	314,198
Net Assets Consist of:
Paid-in-Capital	$	314,130
Total Distributable Earnings		68
Net Assets	$	314,198
CLASS IR:
Net Assets	$	118,335
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		11,831,207
Net Asset Value, Offering and Redemption Price Per Share	$	10.00
INSTITUTIONAL CLASS:
Net Assets	$	9,997
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		998,192
Net Asset Value, Offering and Redemption Price Per Share	$	10.02
CLASS A:
Net Assets	$	185,866
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		18,580,220
Net Asset Value, Offering and Redemption Price Per Share	$	10.00

@  Amount is less than $500.

The accompanying notes are an integral part of the financial statements.
10

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Ultra-Short Municipal Income Portfolio

Statement of Operations	Year Ended September 30, 2020 (000)
Investment Income:
Interest from Securities of Unaffiliated Issuers	$	3,002
Expenses:
Advisory Fees (Note B)		600
Shareholder Services Fees — Institutional Class (Note D)		31
Shareholder Services Fees — Class A (Note D)		379
Administration Fees (Note C)		240
Professional Fees		135
Registration Fees		108
Offering Costs		37
Custodian Fees (Note F)		13
Shareholder Reporting Fees		12
Trustees' Fees and Expenses		7
Pricing Fees		7
Transfer Agency Fees — Class IR (Note E)		2
Transfer Agency Fees — Institutional Class (Note E)		2
Transfer Agency Fees — Class A (Note E)		2
Other Expenses		19
Total Expenses		1,594
Waiver of Advisory Fees (Note B)		(600	)
Expenses Reimbursed by Adviser (Note B)		(188	)
Reimbursement of Class Specific Expenses — Class IR (Note B)		(2	)
Reimbursement of Class Specific Expenses — Institutional Class (Note B)		(2	)
Waiver of Shareholder Servicing Fees — Class A (Note D)		(28	)
Net Expenses		774
Net Investment Income		2,228
Realized Gain:
Investments Sold		—	@
Change in Unrealized Appreciation (Depreciation):
Investments		26
Net Realized Gain and Change in Unrealized Appreciation (Depreciation)		26
Net Increase in Net Assets Resulting from Operations	$	2,254

@  Amount is less than $500.

The accompanying notes are an integral part of the financial statements.
11

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Ultra-Short Municipal Income Portfolio

Statements of Changes in Net Assets	Year Ended September 30, 2020 (000)			Period from December 19, 2018^ to September 30, 2019 (000)
Increase (Decrease) in Net Assets:
Operations:
Net Investment Income	$	2,228		$	1,474
Net Realized Gain (Loss)		—	@		(—	@)
Net Change in Unrealized Appreciation (Depreciation)		26			1
Net Increase in Net Assets Resulting from Operations		2,254			1,475
Dividends and Distributions to Shareholders:
Class IR		(623	)		(483	)
Institutional Class		(317	)		(276	)
Class A		(1,288	)		(715	)
Total Dividends and Distributions to Shareholders		(2,228	)		(1,474	)
Capital Share Transactions:(1)
Class IR:
Subscribed		157,978			96,053
Distributions Reinvested		622			440
Redeemed		(107,472	)		(29,320	)
Institutional Class:
Subscribed		37,600			40,000
Distributions Reinvested		316			235
Redeemed		(68,136	)		—
Class A:
Subscribed		299,894			154,961
Distributions Reinvested		1,286			664
Redeemed		(248,222	)		(22,728	)
Net Increase in Net Assets Resulting from Capital Share Transactions		73,866			240,305
Total Increase in Net Assets		73,892			240,306
Net Assets:
Beginning of Period		240,306			—
End of Period	$	314,198		$	240,306
(1) Capital Share Transactions:
Class IR:
Shares Subscribed		15,800			9,605
Shares Issued on Distributions Reinvested		62			44
Shares Redeemed		(10,748	)		(2,932	)
Net Increase in Class IR Shares Outstanding		5,114			6,717
Institutional Class:
Shares Subscribed		3,756			4,000
Shares Issued on Distributions Reinvested		32			24
Shares Redeemed		(6,813	)		—
Net Increase (Decrease) in Institutional Class Shares Outstanding		(3,025	)		4,024
Class A:
Shares Subscribed		29,992			15,497
Shares Issued on Distributions Reinvested		129			66
Shares Redeemed		(24,830	)		(2,273	)
Net Increase in Class A Shares Outstanding		5,291			13,290

^  Commencement of Operations.

@  Amount is less than $500.

The accompanying notes are an integral part of the financial statements.
12

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Ultra-Short Municipal Income Portfolio

	Class IR
Selected Per Share Data and Ratios	Year Ended September 30, 2020			Period from December 19, 2018(1) to September 30, 2019
Net Asset Value, Beginning of Period	$	10.00		$	10.00
Income from Investment Operations:
Net Investment Income(2)		0.09			0.12
Net Realized and Unrealized Gain		0.00	(3)		0.00	(3)
Total from Investment Operations		0.09			0.12
Distributions from and/or in Excess of:
Net Investment Income		(0.09	)		(0.12	)
Net Asset Value, End of Period	$	10.00		$	10.00
Total Return(4)		0.91	%		1.19	%(5)
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	118,335		$	67,174
Ratio of Expenses Before Expense Limitation		0.40	%		0.52	%(6)
Ratio of Expenses After Expense Limitation		0.13	%		0.13	%(6)
Ratio of Net Investment Income		0.78	%		1.49	%(6)
Portfolio Turnover Rate		N/A(7)			N/A(7)

(1)  Commencement of Operations.

(2)  Per share amount is based on average shares outstanding.

(3)  Amount is less than $0.005 per share.

(4)  Calculated based on the net asset value as of the last business day of the period.

(5)  Not annualized.

(6)  Annualized.

(7)  During the reporting period, the Fund did not hold any long-term investments and accordingly portfolio turnover is not applicable.

The accompanying notes are an integral part of the financial statements.
13

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Ultra-Short Municipal Income Portfolio

	Institutional Class
Selected Per Share Data and Ratios	Year Ended September 30, 2020			Period from December 19, 2018(1) to September 30, 2019
Net Asset Value, Beginning of Period	$	10.00		$	10.00
Income from Investment Operations:
Net Investment Income(2)		0.10			0.11
Net Realized and Unrealized Gain		0.00	(3)		0.00	(3)
Total from Investment Operations		0.10			0.11
Distributions from and/or in Excess of:
Net Investment Income		(0.08	)		(0.11	)
Net Asset Value, End of Period	$	10.02		$	10.00
Total Return(4)		1.01	%		1.11	%(5)
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	9,997		$	40,250
Ratio of Expenses Before Expense Limitation		0.49	%		0.62	%(6)
Ratio of Expenses After Expense Limitation		0.23	%		0.23	%(6)
Ratio of Net Investment Income		1.03	%		1.39	%(6)
Portfolio Turnover Rate		N/A(7)			N/A(7)

(1)  Commencement of Operations.

(2)  Per share amount is based on average shares outstanding.

(3)  Amount is less than $0.005 per share.

(4)  Calculated based on the net asset value as of the last business day of the period.

(5)  Not annualized.

(6)  Annualized.

(7)  During the reporting period, the Fund did not hold any long-term investments and accordingly portfolio turnover is not applicable.

The accompanying notes are an integral part of the financial statements.
14

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Financial Highlights

Ultra-Short Municipal Income Portfolio

	Class A
Selected Per Share Data and Ratios	Year Ended September 30, 2020			Period from December 19, 2018(1) to September 30, 2019
Net Asset Value, Beginning of Period	$	10.00		$	10.00
Income from Investment Operations:
Net Investment Income(2)		0.07			0.10
Net Realized and Unrealized Gain		0.00	(3)		0.00	(3)
Total from Investment Operations		0.07			0.10
Distributions from and/or in Excess of:
Net Investment Income		(0.07	)		(0.10	)
Net Asset Value, End of Period	$	10.00		$	10.00
Total Return(4)		0.73	%		1.04	%(5)
Ratios to Average Net Assets and Supplemental Data:
Net Assets, End of Period (Thousands)	$	185,866		$	132,882
Ratio of Expenses Before Expense Limitation		0.59	%		0.72	%(6)
Ratio of Expenses After Expense Limitation		0.32	%		0.33	%(6)
Ratio of Net Investment Income		0.68	%		1.30	%(6)
Portfolio Turnover Rate		N/A(7)			N/A(7)

(1)  Commencement of Operations.

(2)  Per share amount is based on average shares outstanding.

(3)  Amount is less than $0.005 per share.

(4)  Calculated based on the net asset value as of the last business day of the period.

(5)  Not annualized.

(6)  Annualized.

(7)  During the reporting period, the Fund did not hold any long-term investments and accordingly portfolio turnover is not applicable.

The accompanying notes are an integral part of the financial statements.
15

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements

Morgan Stanley Institutional Fund Trust ("Trust") is registered under the Investment Company Act of 1940, as amended (the "Act"), as an open-end management investment company. The Trust is comprised of twelve separate, active funds (individually referred to as a "Fund," collectively as the "Funds"). The Trust applies investment company accounting and reporting guidance. All Funds are considered diversified for purposes of the Act.

The accompanying financial statements relate to the Ultra-Short Municipal Income Portfolio. The Fund seeks current income exempt from federal income tax and capital preservation while maintaining liquidity. The Fund offers three classes of shares — Class IR, Institutional Class and Class A.

A. Significant Accounting Policies: The following significant accounting policies are in conformity with U.S. generally accepted accounting principles ("GAAP"). Such policies are consistently followed by the Trust in the preparation of its financial statements. GAAP may require management to make estimates and assumptions that affect the reported amounts and disclosures in the financial statements. Actual results may differ from those estimates.

In March 2017, the Financial Accounting Standards Board ("FASB") issued an Accounting Standard Update, ASU 2017-08, Receivables-Nonrefundable Fees and Other Costs (Subtopic 310-20), Premium Amortization on Purchased Callable Debt Securities (the "ASU") which amends the amortization period for certain purchased callable debt securities held at a premium, shortening such period to the earliest call date. The ASU does not require any accounting change for debt securities held at a discount; the discount continues to be amortized to maturity. The ASU is effective for fiscal years, and interim periods within those fiscal years, beginning after December 15, 2018. The Fund has adopted the ASU as of September 30, 2020 and it did not have an impact on the Fund's financial statements.

1.  Security Valuation: (1) Certain portfolio securities may be valued by an outside pricing service/vendor approved by the Trust's Board of Trustees (the "Trustees"). The pricing service/vendor may employ a pricing model that takes into account, among other things, bids, yield spreads and/or other market data and specific security characteristics. Alternatively, if a valuation is not available from an outside pricing service/vendor, and the security trades on an exchange, the security may be valued at its latest reported sale price (or at the exchange official closing price if

such exchange reports an official closing price), prior to the time when assets are valued. If there are no sales on a given day and if there is no official exchange closing price for that day, the security is valued at the mean between the last reported bid and asked prices if such bid and asked prices are available in the relevant exchanges. If only bid prices are available then the latest bid price may be used. If Morgan Stanley Investment Management Inc. (the "Adviser"), a wholly-owned subsidiary of Morgan Stanley, determines that the price provided by the outside pricing service/vendor or exchange does not reflect the security's fair value or is unable to provide a price, prices from brokers or dealers may also be utilized. In these circumstances, the value of the security will be the mean of bid and asked prices obtained from brokers or dealers; and (2) when market quotations are not readily available, including circumstances under which the Adviser determines that the closing price, last sale price or the mean between the last reported bid and asked prices are not reflective of a security's market value, portfolio securities are valued at their fair value as determined in good faith under procedures established by and under the general supervision of the Trustees. Occasionally, developments affecting the closing prices of securities and other assets may occur between the times at which valuations of such securities are determined (that is, close of the foreign market on which the securities trade) and the close of business of the New York Stock Exchange ("NYSE"). If developments occur during such periods that are expected to materially affect the value of such securities, such valuations may be adjusted to reflect the estimated fair value of such securities as of the close of the NYSE, as determined in good faith by the Trustees or by the Adviser using a pricing service and/or procedures approved by the Trustees.

The Trustees have responsibility for determining in good faith the fair value of the investments, and the Trustees may appoint others, such as the Trust's Adviser or a valuation committee, to assist the Trustees in determining fair value and to make the actual calculations pursuant to the fair valuation methodologies previously approved by the Trustees. Under procedures approved by the Trustees, the Trust's Adviser has formed a Valuation Committee whose members are approved by the Trustees. The Valuation Committee provides administration and oversight of the Trust's valuation policies and procedures, which are reviewed at least annually by the Trustees. These procedures allow the

16

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

Trust to utilize independent pricing services, quotations from securities and financial instrument dealers and other market sources to determine fair value.

2.  Fair Value Measurement: FASB Accounting Standards Codification^TM ("ASC") 820, "Fair Value Measurement" ("ASC 820"), defines fair value as the value that the Fund would receive to sell an investment or pay to transfer a liability in a timely transaction with an independent buyer in the principal market, or in the absence of a principal market, the most advantageous market for the investment or liability. ASC 820 establishes a three-tier hierarchy to distinguish between (1) inputs that reflect the assumptions market participants would use in valuing an asset or liability developed based on market data obtained from sources independent of the reporting entity (observable inputs) and (2) inputs that reflect the reporting entity's own assumptions about the assumptions market participants would use in valuing an asset or liability developed based on the best information available in the circumstances (unobservable inputs) and to establish classification of fair value measurements for disclosure purposes. Various inputs are used in determining the value of the Fund's investments. The inputs are summarized in the three broad levels listed below:

•  Level 1 – unadjusted quoted prices in active markets for identical investments

•  Level 2 – other significant observable inputs (including quoted prices for similar investments, interest rates, prepayment speeds, credit risk, etc.)

•  Level 3 – significant unobservable inputs including the Fund's own assumptions in determining the fair value of investments. Factors considered in making this determination may include, but are not limited to, information obtained by contacting the issuer, analysts, or the appropriate stock exchange (for exchange-traded securities), analysis of the issuer's financial statements or other available documents and, if necessary, available information concerning other securities in similar circumstances.

The inputs or methodology used for valuing securities are not necessarily an indication of the risk associated with investing in those securities and the determination

of the significance of a particular input to the fair value measurement in its entirety requires judgment and considers factors specific to each security.

The following is a summary of the inputs used to value the Fund's investments as of September 30, 2020:

Investment Type	Level 1 Unadjusted quoted prices (000)		Level 2 Other significant observable inputs (000)		Level 3 Significant unobservable inputs (000)		Total (000)
Assets:
Short-Term Investments
Weekly Variable Rate Bonds	$	—	$	91,720	$	—	$	91,720
Daily Variable Rate Bonds		—		68,000		—		68,000
Closed-End Investment Companies		—		30,800		—		30,800
Floating Rate Notes		—		39,819		—		39,819
Quarterly Variable Rate Bonds		—		10,606		—		10,606
Semi-Annual Variable Rate Bonds		—		11,500		—		11,500
Commercial Paper		—		45,000		—		45,000
Municipal Bonds & Notes		—		19,401		—		19,401
Total Short-Term Investments		—		316,846		—		316,846
Total Assets	$	—	$	316,846	$	—	$	316,846

Transfers between investment levels may occur as the markets fluctuate and/or the availability of data used in an investment's valuation changes.

3.  Indemnifications: The Trust enters into contracts that contain a variety of indemnifications. The Trust's maximum exposure under these arrangements is unknown. However, the Trust has not had prior claims or losses pursuant to these contracts and expects the risk of loss to be remote.

4.  Dividends and Distributions to Shareholders: Dividends and distributions to shareholders are recorded on the close of each business day. Dividends from net investment income are declared daily and paid monthly. Net realized capital gains, if any, are distributed at least annually.

5.  Security Transactions, Income and Expenses: Security transactions are accounted for on the trade date (date the order to buy or sell is executed). Realized gains and losses on the sale of investment securities are determined on the specific identified cost method. Dividend income and other distributions are recorded on the ex-dividend date (except for certain foreign dividends which may be recorded as soon as the Fund is informed of such

17

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

dividends) net of applicable withholding taxes. Interest income is recognized on the accrual basis except where collection is in doubt. Discounts are accreted and premiums are amortized over the life of the respective securities. Most expenses of the Trust can be directly attributed to a particular Fund. Expenses which cannot be directly attributed are apportioned among the Funds based upon relative net assets or other appropriate methods. Income, expenses (other than class specific expenses — distribution and shareholder services and transfer agency fees) and realized and unrealized gains or losses are allocated to each class of shares based upon their relative net assets.

B. Advisory Fees: The Adviser, a wholly-owned subsidiary of Morgan Stanley, provides the Fund with advisory services under the terms of an Investment Advisory Agreement, paid quarterly, at an annual rate of 0.20% of the average daily net assets of the Fund.

The Adviser has agreed to reduce its advisory fee and/or reimburse the Fund so that total annual Fund operating expenses, excluding certain investment related expenses, taxes, interest and other extraordinary expenses (including litigation), will not exceed 0.25% for Class IR shares, 0.35% for Institutional Class shares and 0.45% for Class A shares. Effective July 1, 2020, the Adviser has agreed to reduce its advisory fee and/or reimburse the Fund so that total annual Fund operating expenses will not exceed 0.40% for Class A shares. The fee waivers and/or expense reimbursements will continue for at least one year from the date of the Fund's prospectus or until such time as the Trustees act to discontinue all or a portion of such waivers and/or reimbursements when they deem such action is appropriate. In addition, the Adviser may make additional voluntary fee waivers and/or expense reimbursements. The ratios of expenses to average net assets disclosed in the Fund's Financial Highlights may be lower than the maximum expense ratios due to these additional fee waivers and/or expense reimbursements. The Adviser may also waive additional advisory fees and/or reimburse expenses to enable the Fund to maintain a minimum level of daily net investment income. For the year ended September 30, 2020, approximately $600,000 of advisory fees were waived and approximately $192,000 of other expenses were reimbursed by the Adviser pursuant to this arrangement.

C. Administration Fees: The Adviser also serves as Administrator to the Trust and provides administrative services pursuant to an Administration Agreement for an annual fee, accrued daily and paid monthly, of 0.08% of the Fund's average daily net assets. Under a Sub-Administration Agreement

between the Administrator and State Street Bank and Trust Company ("State Street"), State Street provides certain administrative services to the Trust. For such services, the Administrator pays State Street a portion of the fee the Administrator receives from the Fund.

D. Shareholder Services Fees: Morgan Stanley Distribution, Inc. ("MSDI" or the "Distributor"), a wholly-owned subsidiary of the Adviser, and an indirect subsidiary of Morgan Stanley, serves as the Trust's Distributor of Fund shares pursuant to a Distribution Agreement. The Trust has adopted a Shareholder Services Plan with respect to the Institutional Class shares pursuant to Rule 12b-1 under the Act. Under the Shareholder Services Plan, the Fund pays the Distributor a shareholder services fee, accrued daily and paid monthly, at an annual rate of 0.10% of the Fund's average daily net assets attributable to the Institutional Class shares.

The Trust has adopted a Shareholder Services Plan with respect to the Class A shares pursuant to Rule 12b-1 under the Act. Under the Shareholder Services Plan, the Fund pays the Distributor a shareholder services fee, accrued daily and paid monthly, at an annual rate of 0.20% of the Fund's average daily net assets attributable to the Class A shares. The Distributor has agreed to waive the 12b-1 fee on Class A shares of the Fund to the extent it exceeds 0.15% of the average daily net assets of such shares on an annualized basis. This waiver will continue for at least one year or until such time as the Trustees act to discontinue all or a portion of such waiver when it deems such action is appropriate. For the year ended September 30, 2020, this waiver amounted to approximately $25,000.

The Distributor has agreed to reduce its distribution fees to enable the Fund to maintain a minimum level of daily net investment income. For the year ended September 30, 2020, this waiver amounted to approximately $3,000.

The shareholder services fees are used to support the expenses associated with servicing and maintaining accounts. The Distributor may compensate other parties for providing shareholder support services to investors who purchase Institutional Class and Class A shares.

E. Dividend Disbursing and Transfer/Co-Transfer Agent: The Trust's dividend disbursing and transfer agent is DST Asset Manager Solutions, Inc. ("DST"). Pursuant to a Transfer Agency Agreement, the Trust pays DST a fee based on the number of classes, accounts and transactions relating to the Funds of the Trust.

18

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

Morgan Stanley Services Company Inc. serves as Co-Transfer Agent and provides certain transfer agency services to the Fund with respect to certain direct transactions with the Fund.

F. Custodian Fees: State Street (the "Custodian") also serves as Custodian for the Trust in accordance with a Custodian Agreement. The Custodian holds cash, securities and other assets of the Trust as required by the Act. Custody fees are payable monthly based on assets held in custody, investment purchases and sales activity and account maintenance fees, plus reimbursement for certain out-of-pocket expenses.

G. Security Transactions and Transactions with Affiliates: The Fund is permitted to purchase and sell securities ("cross-trade") from and to other Morgan Stanley funds as well as other funds and client accounts for which the Adviser or an affiliate of the Adviser serves as investment adviser, pursuant to procedures approved by the Trustees in compliance with Rule 17a-7 under the Act (the "Rule"). Each cross-trade is executed at the current market price in compliance with provisions of the Rule. For the year ended September 30, 2020, the Fund engaged in cross-trade purchases of approximately $18,750,000 and sales of approximately $16,300,000 which resulted in no net realized gains or losses.

The Fund has an unfunded Deferred Compensation Plan (the "Compensation Plan"), which allows each independent Trustee to defer payment of all, or a portion, of the fees he or she receives for serving on the Board of Trustees. Each eligible Trustee generally may elect to have the deferred amounts credited with a return equal to the total return on one or more of the Morgan Stanley funds that are offered as investment options under the Compensation Plan. Appreciation/depreciation and distributions received from these investments are recorded with an offsetting increase/decrease in the deferred compensation obligation and do not affect the NAV of the Fund.

H. Federal Income Taxes: It is the Fund's intention to continue to qualify as a regulated investment company and distribute all of its taxable and tax-exempt income. Accordingly, no provision for federal income taxes is required in the financial statements.

The Fund may be subject to taxes imposed by countries in which it invests. Such taxes are generally based on income and/or capital gains earned or repatriated. Taxes are accrued based on net investment income, net realized gains and net unrealized appreciation as such income and/or gains are earned.

Taxes may also be based on transactions in foreign currency and are accrued based on the value of investments denominated in such currency.

FASB ASC 740-10, "Income Taxes — Overall", sets forth a minimum threshold for financial statement recognition of the benefit of a tax position taken or expected to be taken in a tax return. Management has concluded there are no significant uncertain tax positions that would require recognition in the financial statements. If applicable, the Fund recognizes interest accrued related to unrecognized tax benefits in "Interest Expense" and penalties in "Other Expenses" in the Statement of Operations. The Fund files tax returns with the U.S. Internal Revenue Service, New York and various states. Each of the tax years in the two-year period ended September 30, 2020, remains subject to examination by taxing authorities.

The tax character of distributions paid may differ from the character of distributions shown for GAAP purposes due to short-term capital gains being treated as ordinary income for tax purposes. The tax character of distributions paid during fiscal years 2020 and 2019 was as follows:

2020 Distributions Paid From: Tax-Exempt Income (000)		2019 Distributions Paid From: Tax-Exempt Income (000)
$	2,228	$	1,474

The amount and character of income and gains to be distributed are determined in accordance with income tax regulations which may differ from GAAP. These book/tax differences are either considered temporary or permanent in nature.

Temporary differences are attributable to differing book and tax treatments for the timing of the recognition of gains (losses) on certain investment transactions and the timing of the deductibility of certain expenses.

The Fund had no permanent differences causing reclassifications among the components of net assets for the year ended September 30, 2020.

At September 30, 2020, the components of distributable earnings for the Fund on a tax basis were as follows:

Undistributed Tax-Exempt Income (000)		Undistributed Long-Term Capital Gain (000)
$	189	$	—

19

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Notes to Financial Statements (cont'd)

At September 30, 2020, the Fund had available for federal income tax purposes unused short-term capital losses of approximately $1,000 that do not have an expiration date.

To the extent that capital loss carryforwards are used to offset any future capital gains realized, no capital gains tax liability will be incurred by the Fund for gains realized and not distributed. To the extent that capital gains are offset, such gains will not be distributed to the shareholders.

I. Credit Facility: The Trust and other Morgan Stanley funds participated in a $300,000,000 committed, unsecured revolving line of credit facility (the "Facility") with State Street. This Facility is to be used for temporary emergency purposes or funding of shareholder redemption requests. The interest rate on borrowings is based on the federal funds rate or 1 month LIBOR rate plus a spread. The Facility also has a commitment fee of 0.25% per annum based on the unused portion of the Facility. During the year ended September 30, 2020, the Fund did not have any borrowings under the Facility.

J. Other: At September 30, 2020, the Fund had record owners of 10% or greater. Investment activities of these shareholders could have a material impact on the Fund. The aggregate percentage of such owners was 92.8%.

K. Market Risk: Certain impacts to public health conditions particular to the coronavirus (COVID-19) outbreak could impact the operations and financial performance of certain of the Fund's investments. The extent of the impact to the financial performance of the Fund's investments will depend on future developments, including (i) the duration and spread of the outbreak, (ii) the restrictions and advisories, (iii) the effects on the financial markets, and (iv) the effects on the economy overall, all of which are highly uncertain and cannot be predicted. If the financial performance of the Fund's investments is impacted because of these factors for an extended period, the Fund's investment results may be adversely affected.

20

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Report of Independent Registered Public Accounting Firm

To the Shareholders and Board of Trustees of
Morgan Stanley Institutional Fund Trust —
Ultra-Short Municipal Income Portfolio

Opinion on the Financial Statements

We have audited the accompanying statement of assets and liabilities of Ultra-Short Municipal Income Portfolio (the "Fund") (one of the funds constituting Morgan Stanley Institutional Fund Trust (the "Trust")), including the portfolio of investments, as of September 30, 2020, and the related statement of operations for the year then ended and the statements of changes in net assets and the financial highlights for the year then ended and the period from December 19, 2018 (commencement of operations) through September 30, 2019 and the related notes (collectively referred to as the "financial statements"). In our opinion, the financial statements present fairly, in all material respects, the financial position of Ultra-Short Municipal Income Portfolio (one of the funds constituting Morgan Stanley Institutional Fund Trust) at September 30, 2020, the results of its operations for the year then ended and the changes in its net assets and its financial highlights for the year then ended and the period from December 19, 2018 (commencement of operations) through September 30, 2019, in conformity with U.S. generally accepted accounting principles.

Basis for Opinion

These financial statements are the responsibility of the Trust's management. Our responsibility is to express an opinion on the Fund's financial statements based on our audits. We are a public accounting firm registered with the Public Company Accounting Oversight Board (United States) ("PCAOB") and are required to be independent with respect to the Trust in accordance with the U.S. federal securities law and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB.

We conducted our audits in accordance with the standards of the PCAOB. Those standards require that we plan and perform the audit to obtain reasonable assurance about whether the financial statements are free of material misstatement, whether due to error or fraud. The Trust is not required to have, nor were we engaged to perform, an audit of the Trust's internal control over financial reporting. As part of our audits, we are required to obtain an understanding of internal control over financial reporting, but not for the purpose of expressing an opinion on the effectiveness of the Trust's internal control over financial reporting. Accordingly, we express no such opinion.

Our audits included performing procedures to assess the risks of material misstatement of the financial statements, whether due to error or fraud, and performing procedures that respond to those risks. Such procedures included examining, on a test basis, evidence regarding the amounts and disclosures in the financial statements. Our procedures included confirmation of securities owned as of September 30, 2020 by correspondence with the custodian and brokers or by other appropriate auditing procedures where replies from brokers were not received. Our audits also included evaluating the accounting principles used and significant estimates made by management, as well as evaluating the overall presentation of the financial statements. We believe that our audits provide a reasonable basis for our opinion.

We have served as the auditor of one or more Morgan Stanley investment companies since 2000.
Boston, Massachusetts
November 24, 2020

21

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Advisory Agreement Approval (unaudited)

Nature, Extent and Quality of Services

The Board reviewed and considered the nature and extent of the investment advisory services provided by the Adviser under the advisory agreement, including portfolio management, investment research and equity and fixed income securities trading. The Board also reviewed and considered the nature and extent of the non-advisory, administrative services provided by the Administrator under the administration agreement, including accounting, operations, clerical, bookkeeping, compliance, business management and planning, legal services and the provision of supplies, office space and utilities at the Adviser's expense. The Board also considered the Adviser's investment in personnel and infrastructure that benefits the Fund. (The Adviser and Administrator together are referred to as the "Adviser" and the advisory and administration agreements together are referred to as the "Management Agreement.") The Board also considered that the Adviser serves a variety of other investment advisory clients and has experience overseeing service providers. The Board also compared the nature of the services provided by the Adviser with similar services provided by non-affiliated advisers as prepared by Broadridge Financial Solutions, Inc. ("Broadridge").

The Board reviewed and considered the qualifications of the portfolio managers, the senior administrative managers and other key personnel of the Adviser who provide the advisory and administrative services to the Fund. The Board determined that the Adviser's portfolio managers and key personnel are well qualified by education and/or training and experience to perform the services in an efficient and professional manner. The Board concluded that the nature and extent of the advisory and administrative services provided were necessary and appropriate for the conduct of the business and investment activities of the Fund and supported its decision to approve the Management Agreement.

Performance, Fees and Expenses of the Fund

The Board reviewed the performance, fees and expenses of the Fund compared to its peers, as prepared by Broadridge, and to appropriate benchmarks where applicable. The Board discussed with the Adviser the performance goals and the actual results achieved in managing the Fund. When considering a fund's performance, the Board and the Adviser place emphasis on trends and longer-term returns (focusing on one-year, three-year and five-year performance, as of December 31, 2019, or since inception, as applicable). When a fund underperforms its benchmark and/or its peer group average, the Board and the Adviser discuss the causes of such underperformance and, where necessary, they discuss specific changes to investment strategy or investment personnel. The Board noted that the Fund's performance was below its peer group average for one-year period and the period since the middle of December 2018, the month of the Fund's inception. The Board discussed with the Adviser the level of the advisory and administration fees (together, the "management fee") for this Fund relative to comparable funds and/or other accounts advised by the Adviser and/or compared to its peers as prepared by Broadridge. In addition to the management fee, the Board also reviewed the Fund's total expense ratio. The Board noted that the Fund's management fee and total expense ratio were lower than its peer group averages. After discussion, the Board concluded that the Fund's (i) performance was acceptable and (ii) management fee and total expense ratio were competitive with its peer group averages.

Economies of Scale

The Board considered the size and growth prospects of the Fund and how that relates to the Fund's total expense ratio and particularly the Fund's management fee rate, which does not include a breakpoint. In conjunction with its review of the Adviser's profitability, the Board discussed with the Adviser how a change in assets can affect the efficiency or effectiveness of managing the Fund and whether the management fee level is appropriate relative to current and projected asset levels and/or whether the management fee structure reflects economies of scale as asset levels change. The Board has determined that its review of the actual and/or potential economies of scale of the Fund supports its decision to approve the Management Agreement.

Profitability of the Adviser and Affiliates

The Board considered information concerning the costs incurred and profits realized by the Adviser and its affiliates during the last year from their relationship with the Fund and during the last two years from their relationship with the Morgan Stanley Fund Complex and reviewed with the Adviser the cost allocation methodology used to determine the profitability of the Adviser and affiliates. The Board has determined that its review of the analysis of the Adviser's expenses and profitability supports its decision to approve the Management Agreement.

22

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Investment Advisory Agreement Approval (unaudited) (cont'd)

Other Benefits of the Relationship

The Board considered other direct and indirect benefits to the Adviser and/or its affiliates derived from their relationship with the Fund and other funds advised by the Adviser. These benefits may include, among other things, fees for trading, distribution and/or shareholder servicing and for transaction processing and reporting platforms used by securities lending agents, and research received by the Adviser generated from commission dollars spent on funds' portfolio trading. The Board reviewed with the Adviser these arrangements and the reasonableness of the Adviser's costs relative to the services performed. The Board has determined that its review of the other benefits received by the Adviser or its affiliates supports its decision to approve the Management Agreement.

Resources of the Adviser and Historical Relationship Between the Fund and the Adviser

The Board considered whether the Adviser is financially sound and has the resources necessary to perform its obligations under the Management Agreement. The Board also reviewed and considered the historical relationship between the Fund and the Adviser, including the organizational structure of the Adviser, the policies and procedures formulated and adopted by the Adviser for managing the Fund's operations and the Board's confidence in the competence and integrity of the senior managers and key personnel of the Adviser. The Board concluded that the Adviser has the financial resources necessary to fulfill its obligations under the Management Agreement and that it is beneficial for the Fund to continue its relationship with the Adviser.

Other Factors and Current Trends

The Board considered the controls and procedures adopted and implemented by the Adviser and monitored by the Fund's Chief Compliance Officer and concluded that the conduct of business by the Adviser indicates a good faith effort on its part to adhere to high ethical standards in the conduct of the Fund's business.

As part of the Board's review, the Board received information from management on the impact of COVID-19 on the firm generally and the Adviser and the Fund in particular including, among other information, the pandemic's current and expected impact on the Fund's performance and operations.

General Conclusion

After considering and weighing all of the above factors, with various written materials and verbal information presented by the Adviser, the Board concluded that it would be in the best interest of the Fund and its shareholders to approve renewal of the Management Agreement for another year. In reaching this conclusion the Board did not give particular weight to any single piece of information or factor referenced above. The Board considered these factors and information over the course of the year and in numerous meetings, some of which were in executive session with only the independent Board members and their counsel present. It is possible that individual Board members may have weighed these factors, and the information presented, differently in reaching their individual decisions to approve the Management Agreement.

23

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Liquidity Risk Management Program (unaudited)

In compliance with Rule 22e-4 under the Investment Company Act of 1940, as amended (the "Liquidity Rule"), the Fund has adopted and implemented a liquidity risk management program (the "Program"), which is reasonably designed to assess and manage the risk that the Fund could not meet requests to redeem shares issued by the Fund without significant dilution of remaining investors' interests in the Fund (i.e., liquidity risk). The Fund's Board of Trustees (the "Board") previously approved the designation of the Liquidity Risk Subcommittee (the "LRS") as Program administrator. The LRS is comprised of representatives from various divisions within Morgan Stanley Investment Management.

At a meeting held on April 22-23, 2020, the Board reviewed a written report prepared by the LRS that addressed the Program's operation and assessed its adequacy, and effectiveness of implementation for the period from December 1, 2018, through December 31, 2019, as required under the Liquidity Rule. The report concluded that the Program operated effectively and was adequately and effectively implemented in all material aspects, and that the relevant controls and safeguards were appropriately designed to enable the LRS to administer the Program in compliance with the Liquidity Rule.

In accordance with the Program, the LRS assessed each Fund's liquidity risk no less frequently than annually taking into consideration certain factors, as applicable, such as (i) investment strategy and liquidity of portfolio investments, (ii) short-term and long-term cash flow projections and (iii) holdings of cash and cash equivalents and borrowing arrangements and other funding sources. Certain factors are considered under both normal and reasonably foreseeable stressed conditions.

Each Fund portfolio investment is classified into one of four liquidity categories, which classification is assessed at least monthly by the LRS. The classification is based on a determination of the number of days it is reasonably expected to take to convert the investment into cash, or sell or dispose of the investment, in current market conditions without significantly changing the market value of the investment. Liquidity classification determinations take into account various market, trading and investment-specific considerations, as well as market depth, and in some cases utilize third-party vendor data.

The Liquidity Rule limits a fund's investments in illiquid investments to 15% of its net assets and requires funds that do not primarily hold assets that are highly liquid investments to determine and maintain a minimum percentage of the fund's net assets to be invested in highly liquid investments (highly liquid investment minimum or "HLIM"). The LRS believes that the Program includes provisions reasonably designed to review, monitor and comply with the 15% limit on illiquid investments and for determining, periodically reviewing and complying with the HLIM requirement, as applicable.

There can be no assurance that the Program will achieve its objectives under all circumstances in the future. Please refer to the Fund's prospectus for more information regarding the Fund's exposure to liquidity risk and other risks to which it may be subject.

24

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Federal Tax Notice (unaudited)

For federal income tax purposes, the following information is furnished with respect to the distributions paid by the Fund during its taxable year ended September 30, 2020. The Fund designated 100.0% of its income dividends as tax-exempt income dividends.

In January, the Fund provides tax information to shareholders for the preceding calendar year.

25

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Privacy Notice (unaudited)  April 2019

FACTS	WHAT DOES MSIM DO WITH YOUR PERSONAL INFORMATION?
Why?	Financial companies choose how they share your personal information. Federal law gives consumers the right to limit some but not all sharing. Federal law also requires us to tell you how we collect, share, and protect your personal information. Please read this notice carefully to understand what we do.
What?	The types of personal information we collect and share depend on the product or service you have with us. This information can include: n Social Security number and income n investment experience and risk tolerance n checking account number and wire transfer instructions
How?	All financial companies need to share customers' personal information to run their everyday business. In the section below, we list the reasons financial companies can share their customers' personal information; the reasons MSIM chooses to share; and whether you can limit this sharing.

Reasons we can share your personal information	Does MSIM share?	Can you limit this sharing?
For our everyday business purposes — such as to process your transactions, maintain your account(s), respond to court orders and legal investigations, or report to credit bureaus	Yes	No
For our marketing purposes — to offer our products and services to you	Yes	No
For joint marketing with other financial companies	No	We don't share
For our affiliates' everyday business purposes — information about your transactions and experiences	Yes	No
For our affiliates' everyday business purposes — information about your creditworthiness	No	We don't share
For our affiliates to market to you	No	We don't share
For non-affiliates to market to you	No	We don't share

Questions?Call toll-free (844) 312-6327 or email: imprivacyinquiries@morganstanley.com

26

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Privacy Notice (unaudited) (cont'd)  April 2019

Who we are

Who is providing this notice? Morgan Stanley Investment Management, Inc. and its affiliated registered investment advisers, registered broker-dealers, and registered and unregistered funds ("MSIM")

What we do

How does MSIM protect my personal information?	To protect your personal information from unauthorized access and use, we use security measures that comply with federal law. These measures include computer safeguards and secured files and buildings. We have policies governing the proper handling of customer information by personnel and requiring third parties that provide support to adhere to appropriate security standards with respect to such information.
How does MSIM collect my personal information?	We collect your personal information, for example, when you n open an account or make deposits or withdrawals from your account n buy securities from us or make a wire transfer n give us your contact information We also collect your personal information from others, such as credit bureaus, affiliates, or other companies.
Why can't I limit all sharing?	Federal law gives you the right to limit only n sharing for affiliates' everyday business purposes — information about your creditworthiness n affiliates from using your information to market to you n sharing for non-affiliates to market to you State laws and individual companies may give you additional rights to limit sharing. See below for more on your rights under state law.

Definitions

Affiliates	Companies related by common ownership or control. They can be financial and non-financial companies. n Our affiliates include companies with a Morgan Stanley name and financial companies such as Morgan Stanley Smith Barney LLC and Morgan Stanley & Co.
Non-affiliates	Companies not related by common ownership or control. They can be financial and non-financial companies. n MSIM does not share with non-affiliates so they can market to you.
Joint marketing	A formal agreement between non-affiliated financial companies that together market financial products or services to you. n MSIM doesn't jointly market

Other Important Information

Vermont: Except as permitted by law, we will not share personal information we collect about Vermont residents with Non-affiliates unless you provide us with your written consent to share such information.

California: Except as permitted by law, we will not share personal information we collect about California residents with Non-affiliates and we will limit sharing such personal information with our Affiliates to comply with California privacy laws that apply to us.

27

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited)

Independent Trustees:

Name, Address and Birth Year of Independent Trustee	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years and Other Relevant Professional Experience	Number of Funds in Fund Complex Overseen by Independent Trustee**		Other Directorships Held by Independent Trustee***
Frank L. Bowman c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1944	Trustee	Since August 2006	President, Strategic Decisions, LLC (consulting) (since February 2009); Director or Trustee of various Morgan Stanley Funds (since August 2006); Chairperson of the Compliance and Insurance Committee (since October 2015); formerly, Chairperson of the Insurance Sub-Committee of the Compliance and Insurance Committee (2007-2015); served as President and Chief Executive Officer of the Nuclear Energy Institute (policy organization) (February 2005-November 2008); retired as Admiral, U.S. Navy after serving over 38 years on active duty including 8 years as Director of the Naval Nuclear Propulsion Program in the Department of the Navy and the U.S. Department of Energy (1996-2004); served as Chief of Naval Personnel (July 1994-September 1996) and on the Joint Staff as Director of Political Military Affairs (June 1992-July 1994); knighted as Honorary Knight Commander of the Most Excellent Order of the British Empire; awarded the Officier de l'Orde National du Mérite by the French Government; elected to the National Academy of Engineering (2009).		86	Director of Naval and Nuclear Technologies LLP; Director Emeritus of the Armed Services YMCA; Member of the National Security Advisory Council of the Center for U.S. Global Engagement and a member of the CNA Military Advisory Board; Trustee of Fairhaven United Methodist Church; Member of the Board of Advisors of the Dolphin Scholarship Foundation; Director of other various non-profit organizations; Formerly, Director of BP p.l.c. (November 2010-May 2019).
Kathleen A. Dennis c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1953	Trustee	Since August 2006	President, Cedarwood Associates (mutual fund and investment management consulting) (since July 2006); Chairperson of the Liquidity and Alternatives Sub-Committee of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 2006); formerly, Senior Managing Director of Victory Capital Management (1993-2006).		86	Director of various non-profit organizations.
Nancy C. Everett c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1955	Trustee	Since January 2015	Chief Executive Officer, Virginia Commonwealth University Investment Company (since November 2015); Owner, OBIR, LLC (institutional investment management consulting) (since June 2014); formerly, Managing Director, BlackRock, Inc. (February 2011-December 2013); and Chief Executive Officer, General Motors Asset Management (a/k/a Promark Global Advisors, Inc.) (June 2005-May 2010).		87	Formerly, Member of Virginia Commonwealth University School of Business Foundation (2005-2016); Member of Virginia Commonwealth University Board of Visitors (2013-2015); Member of Committee on Directors for Emerging Markets Growth Fund, Inc. (2007-2010); Chairperson of Performance Equity Management, LLC (2006-2010); and Chairperson, GMAM Absolute Return Strategies Fund, LLC (2006-2010).

28

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Address and Birth Year of Independent Trustee	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years and Other Relevant Professional Experience	Number of Funds in Fund Complex Overseen by Independent Trustee**		Other Directorships Held by Independent Trustee***
Jakki L. Haussler c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1957	Trustee	Since January 2015	Chairman, Opus Capital Group (since January 1996); formerly, Chief Executive Officer, Opus Capital Group (1996-2019); Director, Capvest Venture Fund, LP (May 2000-December 2011); Partner, Adena Ventures, LP (July 1999-December 2010); Director, The Victory Funds (February 2005-July 2008).		87	Director of Service Corporation International and Member, Audit Committee and Investment Committee; Director of Cincinnati Bell Inc. and Member, Audit Committee and Governance and Nominating Committee; Director of Northern Kentucky University Foundation and Member, Investment Committee; Member of Chase College of Law Transactional Law Practice Center Board of Advisors; Director of Chase College of Law Board of Visitors; formerly, Member, University of Cincinnati Foundation Investment Committee; Member, Miami University Board of Visitors (2008-2011); Trustee of Victory Funds (2005-2008) and Chairman, Investment Committee (2007-2008); Member, Service Provider Committee (2005-2008) and Director of Best Transport (2006-2019).
Dr. Manuel H. Johnson c/o Johnson Smick International, Inc. 220 I Street, NE — Suite 200 Washington, D.C. 20002 Birth Year 1949	Trustee	Since July 1991	Senior Partner, Johnson Smick International, Inc. (consulting firm); Chairperson of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since July 1991); Co-Chairman and a founder of the Group of Seven Council (G7C) (international economic commission); formerly, Chairperson of the Audit Committee (July 1991-September 2006), Vice Chairman of the Board of Governors of the Federal Reserve System and Assistant Secretary of the U.S. Treasury.		86	Director of NVR, Inc. (home construction).
Joseph J. Kearns c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1942	Trustee	Since August 1994	Senior Adviser, Kearns & Associates LLC (investment consulting); Chairperson of the Audit Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 1994); Director, Rubicorn Investments (since February 2019); formerly, Deputy Chairperson of the Audit Committee (July 2003-September 2006) and Chairperson of the Audit Committee of various Morgan Stanley Funds (since August 1994); CFO of the J. Paul Getty Trust (1982-1999).		87	Prior to August 10, 2016, Director of Electro Rent Corporation (equipment leasing); Prior to December 31, 2013, Director of The Ford Family Foundation.

29

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Address and Birth Year of Independent Trustee	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years and Other Relevant Professional Experience	Number of Funds in Fund Complex Overseen by Independent Trustee**		Other Directorships Held by Independent Trustee***
Michael F. Klein c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1958	Trustee	Since August 2006	Managing Director, Aetos Alternatives Management, LP (since March 2000); Co-President, Aetos Alternatives Management, LP (since January 2004) and Co-Chief Executive Officer of Aetos Alternatives Management, LP (since August 2013); Chairperson of the Fixed Income Sub-Committee of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 2006); formerly, Managing Director, Morgan Stanley & Co. Inc. and Morgan Stanley Dean Witter Investment Management and President, various Morgan Stanley Funds (June 1998-March 2000); Principal, Morgan Stanley & Co. Inc. and Morgan Stanley Dean Witter Investment Management (August 1997-December 1999).		86	Director of certain investment funds managed or sponsored by Aetos Alternatives Management, LP; Director of Sanitized AG and Sanitized Marketing AG (specialty chemicals).
Patricia Maleski c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1960	Trustee	Since January 2017	Managing Director, JPMorgan Asset Management (2004-2016); Oversight and Control Head of Fiduciary and Conflicts of Interest Program (2015-2016); Chief Control Officer-Global Asset Management (2013-2015); President, JPMorgan Funds (2010-2013); Chief Administrative Officer (2004-2013); various other positions including Treasurer and Board Liaison (since 2001).		87	None.
W. Allen Reed c/o Perkins Coie LLP Counsel to the Independent Trustees 1155 Avenue of the Americas, 22nd Floor New York, NY 10036 Birth Year 1947	Chair of the Board and Trustee	Chair of the Boards since August 2020 and Trustee since August 2006	Chair of the Boards of various Morgan Stanley Funds (since August 2020); Chairperson of the Governance Committee; Chairperson of the Equity Sub-Committee of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 2006); formerly, Vice Chair of the Boards of various Morgan Stanley Funds (January 2020-August 2020); President and Chief Executive Officer of General Motors Asset Management; Chairman and Chief Executive Officer of the GM Trust Bank and Corporate Vice President of General Motors Corporation (August 1994-December 2005).		86	Formerly, Director of Legg Mason, Inc. (2006-2019); and Director of the Auburn University Foundation (2010-2015).

*  This is the earliest date the Trustee began serving the Morgan Stanley Funds. Each Trustee serves an indefinite term, until his or her successor is elected.

**  The Fund Complex includes (as of December 31, 2019) all open-end and closed-end funds (including all of their portfolios) advised by Morgan Stanley Investment Management Inc. (the "Adviser") and any funds that have an adviser that is an affiliated person of the Adviser (including, but not limited to, Morgan Stanley AIP GP LP).

***  This includes any directorships at public companies and registered investment companies held by the Trustee at any time during the past five years.

30

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Trustee and Officer Information (unaudited) (cont'd)

Executive Officers:

Name, Address and Birth Year of Executive Officer	Position(s) Held with Registrant	Length of Time Served*	Principal Occupation(s) During Past 5 Years
John H. Gernon 522 Fifth Avenue New York, NY 10036 Birth Year 1963	President and Principal Executive Officer	Since September 2013	President and Principal Executive Officer of the Equity and Fixed Income Funds and the Morgan Stanley AIP Funds (since September 2013) and the Liquidity Funds and various money market funds (since May 2014) in the Fund Complex; Managing Director of the Adviser; Head of Public Markets Product Development (since 2006).
Timothy J. Knierim 522 Fifth Avenue New York, NY 10036 Birth Year 1959	Chief Compliance Officer	Since December 2016	Managing Director of the Adviser and various entities affiliated with the Adviser; Chief Compliance Officer of various Morgan Stanley Funds and the Adviser (since December 2016) and Chief Compliance Officer of Morgan Stanley AIP GP LP (since 2014). Formerly, Managing Director and Deputy Chief Compliance Officer of the Adviser (2014-2016); and formerly, Chief Compliance Officer of Prudential Investment Management, Inc. (2007-2014).
Francis J. Smith 522 Fifth Avenue New York, NY 10036 Birth Year 1965	Treasurer and Principal Financial Officer	Treasurer since July 2003 and Principal Financial Officer since September 2002	Managing Director of the Adviser and various entities affiliated with the Adviser; Treasurer (since July 2003) and Principal Financial Officer of various Morgan Stanley Funds (since September 2002).
Mary E. Mullin 522 Fifth Avenue New York, NY 10036 Birth Year 1967	Secretary	Since June 1999	Managing Director of the Adviser; Secretary of various Morgan Stanley Funds (since June 1999).
Michael J. Key 522 Fifth Avenue New York, NY 10036 Birth Year 1979	Vice President	Since June 2017	Vice President of the Equity and Fixed Income Funds, Liquidity Funds, various money market funds and the Morgan Stanley AIP Funds in the Fund Complex (since June 2017); Executive Director of the Adviser; Head of Product Development for Equity and Fixed Income Funds (since August 2013).

*  This is the earliest date the officer began serving the Morgan Stanley Funds. Each officer serves a one-year term, until his or her successor is elected and qualifies.

31

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2020

Adviser and Administrator

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

Distributor

Morgan Stanley Distribution, Inc.
522 Fifth Avenue
New York, New York 10036

Dividend Disbursing and Transfer Agent

DST Asset Manager Solutions, Inc.
2000 Crown Colony Drive
Quincy, Massachusetts 02169

Co-Transfer Agent

Morgan Stanley Services Company, Inc.
522 Fifth Avenue
New York, New York 10036

Custodian

State Street Bank and Trust Company
One Lincoln Street
Boston, Massachusetts 02111

Legal Counsel

Dechert LLP
1095 Avenue of the Americas
New York, New York 10036

Counsel to the Independent Trustees

Perkins Coie LLP
1155 Avenue of the Americas,
22nd Floor
New York, New York 10036

Independent Registered Public Accounting Firm

Ernst & Young LLP
200 Clarendon Street
Boston, Massachusetts 02116

Reporting to Shareholders

Each Morgan Stanley fund provides a complete schedule of portfolio holdings in its Semi-Annual and the Annual Reports within 60 days of the end of the fund's second and fourth fiscal quarters. The Semi-Annual and Annual Reports are filed electronically with the Securities and Exchange Commission ("SEC") on Form N-CSRS and Form N-CSR, respectively. Morgan Stanley also delivers the Semi-Annual and Annual Reports to fund shareholders and makes these reports available on its public website, www.morganstanley.com/im/shareholderreports. Each Morgan Stanley non-money market fund also files a complete schedule of portfolio holdings with the SEC for the fund's first and third fiscal quarters as an attachment to Form N-PORT. Morgan Stanley does not deliver the reports for the first and third fiscal quarters to shareholders, nor are the reports posted to the Morgan Stanley public website. However, the holdings for each money market fund are posted to the Morgan Stanley public website. You may obtain the Form N-PORT filings (as well as the Form N-CSR and N-CSRS filings) by accessing the SEC's website, www.sec.gov. You can also request copies of these materials, upon payment of a duplicating fee, by electronic request at the SEC's email address (publicinfo@sec.gov).

Proxy Voting Policies and Procedures and Proxy Voting Record

You may obtain a copy of the Trust's Proxy Voting Policy and Procedures and information regarding how the Trust voted proxies relating to portfolio securities during the most recent twelve-month period ended June 30, without charge, upon request, by calling toll free 1 (800) 548-7786 or by visiting our website at www.morganstanley.com/im/shareholderreports. This information is also available on the SEC's website at www.sec.gov.

This report is authorized for distribution only when preceded or accompanied by a prospectus or summary prospectus of the applicable Fund of Morgan Stanley Institutional Fund Trust, which describes in detail the Fund's investment policies, risks, fees and expenses. Please read the prospectus carefully before you invest or send money. For additional information, including information regarding the investments comprising the Fund, please visit our website at www.morganstanley.com/im/shareholderreports or call toll free 1 (800) 548-7786.

32

Printed in U.S.A.
This Report has been prepared for shareholders and may be distributed to others only if preceded or accompanied by a current prospectus.

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

© 2020 Morgan Stanley. Morgan Stanley Distribution, Inc.

IFTUSMIANN
3300495 EXP 11.30.21

Item 2. Code of Ethics.

(a)       The registrant has adopted a code of ethics (the "Code of Ethics") that applies to its principal executive officer, principal financial officer, principal accounting officer or controller, or persons performing similar functions, regardless of whether these individuals are employed by the registrant or a third party.

(b)       No information need be disclosed pursuant to this paragraph.

(c)       Not applicable.

(d)       Not applicable.

(e)       Not applicable.

(f)       

(1)       The registrant’s Code of Ethics is attached hereto as Exhibit 13 A.

(2)       Not applicable.

(3)       Not applicable.

Item 3. Audit Committee Financial Expert.

The registrant's Board of Trustees has determined that Joseph J. Kearns, an “independent” Trustee, is an “audit committee financial expert" serving on its audit committee. Under applicable securities laws, a person who is determined to be an audit committee financial expert will not be deemed an "expert" for any purpose, including without limitation for the purposes of Section 11 of the Securities Act of 1933, as a result of being designated or identified as an audit committee financial expert. The designation or identification of a person as an audit committee financial expert does not impose on such person any duties, obligations, or liabilities that are greater than the duties, obligations, and liabilities imposed on such person as a member of the audit committee and Board of Trustees in the absence of such designation or identification.

Item 4. Principal Accountant Fees and Services.

(a)(b)(c)(d) and (g). Based on fees billed for the periods shown:

2020

	Registrant			Covered Entities(1)
Audit Fees	$	734,650			N/A
Non-Audit Fees
Audit-Related Fees	$	—	(2)	$	—	(2)
Tax Fees	$	—	(3)	$	306,320	(4)
All Other Fees	$	—		$	30,000	(5)
Total Non-Audit Fees	$	—		$	336,320
Total	$	734,650		$	336,320

2019

	Registrant			Covered Entities(1)
Audit Fees	$	570,650			N/A
Non-Audit Fees
Audit-Related Fees	$	—	(2)	$	—	(2)
Tax Fees	$	53,684	(3)	$	507,296	(4)
All Other Fees	$	—		$	144,110	(5)
Total Non-Audit Fees	$	53,684		$	651,406
Total	$	624,334		$	651,406

_______________________________

N/A- Not applicable, as not required by Item 4.

(1)	Covered Entities include the Adviser (excluding sub-advisors) and any entity controlling, controlled by or under common control with the Adviser that provides ongoing services to the Registrant.
(2)	Audit-Related Fees represent assurance and related services provided that are reasonably related to the performance of the audit of the financial statements of the Covered Entities' and funds advised by the Adviser or its affiliates, specifically data verification and agreed-upon procedures related to asset securitizations and agreed-upon procedures engagements.
(3)	Tax Fees represent tax compliance, tax planning and tax advice services provided in connection with the preparation and review of the Registrant’s tax returns.
(4)	Tax Fees represent tax compliance, tax planning and tax advice services provided in connection with the review of Covered Entities' tax returns.
(5)	All other fees represent project management for future business applications and improving business and operational processes.

(e)(1) The audit committee’s pre-approval policies and procedures are as follows:

AUDIT COMMITTEE

AUDIT AND NON-AUDIT SERVICES

PRE-APPROVAL POLICY AND PROCEDURES

OF THE

MORGAN STANLEY FUNDS

AS ADOPTED AND AMENDED JULY 23, 2004 AND JUNE 12 AND 13, 2019³

1. Statement of Principles

The Audit Committee of the Board is required to review and, in its sole discretion, pre-approve all Covered Services to be provided by the Independent Auditors to the Fund and Covered Entities in order to assure that services performed by the Independent Auditors do not impair the auditor’s independence from the Fund.

The SEC has issued rules specifying the types of services that an independent auditor may not provide to its audit client, as well as the audit committee’s administration of the engagement of the independent auditor. The SEC’s rules establish two different approaches to pre-approving services, which the SEC considers to be equally valid. Proposed services either: may be pre-approved without consideration of specific case-by-case services by the Audit Committee (“general pre-approval”); or require the specific pre-approval of the Audit Committee or its delegate (“specific pre-approval”). The Audit Committee believes that the combination of these two approaches in this Policy will result in an effective and efficient procedure to pre-approve services performed by the Independent Auditors. As set forth in this Policy, unless a type of service has received general pre-approval, it will require specific pre-approval by the Audit Committee (or by any member of the Audit Committee to which pre-approval authority has been delegated) if it is to be provided by the Independent Auditors. Any proposed services exceeding pre-approved cost levels or budgeted amounts will also require specific pre-approval by the Audit Committee.

The appendices to this Policy describe the Audit, Audit-related, Tax and All Other services that have the general pre-approval of the Audit Committee. The term of any general pre-approval is 12 months from the date of pre-approval, unless the Audit Committee considers and provides a different period and states otherwise. The Audit Committee will annually review and pre-approve the services that may be provided by the Independent Auditors without obtaining specific pre-approval from the Audit Committee. The Audit Committee will add to or subtract from the list of general pre-approved services from time to time, based on subsequent determinations.

The purpose of this Policy is to set forth the policy and procedures by which the Audit Committee intends to fulfill its responsibilities. It does not delegate the Audit Committee’s responsibilities to pre-approve services performed by the Independent Auditors to management.

The Fund’s Independent Auditors have reviewed this Policy and believes that implementation of the Policy will not adversely affect the Independent Auditors’ independence.

³        This Audit Committee Audit and Non-Audit Services Pre-Approval Policy and Procedures (the “Policy”), adopted as of the date above, supersedes and replaces all prior versions that may have been adopted from time to time.

2. Delegation

As provided in the Act and the SEC’s rules, the Audit Committee may delegate either type of pre-approval authority to one or more of its members. The member to whom such authority is delegated must report, for informational purposes only, any pre-approval decisions to the Audit Committee at its next scheduled meeting.

3. Audit Services

The annual Audit services engagement terms and fees are subject to the specific pre-approval of the Audit Committee. Audit services include the annual financial statement audit and other procedures required to be performed by the Independent Auditors to be able to form an opinion on the Fund’s financial statements. These other procedures include information systems and procedural reviews and testing performed in order to understand and place reliance on the systems of internal control, and consultations relating to the audit. The Audit Committee will approve, if necessary, any changes in terms, conditions and fees resulting from changes in audit scope, Fund structure or other items.

In addition to the annual Audit services engagement approved by the Audit Committee, the Audit Committee may grant general pre-approval to other Audit services, which are those services that only the Independent Auditors reasonably can provide. Other Audit services may include statutory audits and services associated with SEC registration statements (on Forms N-1A, N-2, N-3, N-4, etc.), periodic reports and other documents filed with the SEC or other documents issued in connection with securities offerings.

The Audit Committee has pre-approved the Audit services in Appendix A. All other Audit services not listed in Appendix A must be specifically pre-approved by the Audit Committee (or by any member of the Audit Committee to which pre-approval has been delegated).

4. Audit-related Services

Audit-related services are assurance and related services that are reasonably related to the performance of the audit or review of the Fund’s financial statements and, to the extent they are Covered Services, the Covered Entities or that are traditionally performed by the Independent Auditors. Because the Audit Committee believes that the provision of Audit-related services does not impair the independence of the auditor and is consistent with the SEC’s rules on auditor independence, the Audit Committee may grant general pre-approval to Audit-related services. Audit-related services include, among others, accounting consultations related to accounting, financial reporting or disclosure matters not classified as “Audit services”; assistance with understanding and implementing new accounting and financial reporting guidance from rulemaking authorities; agreed-upon or expanded audit procedures related to accounting and/or billing records required to respond to or comply with financial, accounting or regulatory reporting matters; and assistance with internal control reporting requirements under Forms N-CEN and/or N-CSR.

The Audit Committee has pre-approved the Audit-related services in Appendix A. All other Audit-related services not listed in Appendix A must be specifically pre-approved by the Audit Committee (or by any member of the Audit Committee to which pre-approval has been delegated).

5. Tax Services

The Audit Committee believes that the Independent Auditors can provide Tax services to the Fund and, to the extent they are Covered Services, the Covered Entities, such as tax compliance, tax planning and tax advice without impairing the auditor’s independence, and the SEC has stated that the Independent Auditors may provide such services.

Pursuant to the preceding paragraph, the Audit Committee has pre-approved the Tax Services in Appendix A. All Tax services in Appendix A must be specifically pre-approved by the Audit Committee (or by any member of the Audit Committee to which pre-approval has been delegated).

6. All Other Services

The Audit Committee believes, based on the SEC’s rules prohibiting the Independent Auditors from providing specific non-audit services, that other types of non-audit services are permitted. Accordingly, the Audit Committee believes it may grant general pre-approval to those permissible non-audit services classified as All Other services that it believes are routine and recurring services, would not impair the independence of the auditor and are consistent with the SEC’s rules on auditor independence.

The Audit Committee has pre-approved the All Other services in Appendix A. Permissible All Other services not listed in Appendix A must be specifically pre-approved by the Audit Committee (or by any member of the Audit Committee to which pre-approval has been delegated).

7. Pre-Approval Fee Levels or Budgeted Amounts

Pre-approval fee levels or budgeted amounts for all services to be provided by the Independent Auditors will be established annually by the Audit Committee. Any proposed services exceeding these levels or amounts will require specific pre-approval by the Audit Committee. The Audit Committee is mindful of the overall relationship of fees for audit and non-audit services in determining whether to pre-approve any such services.

8. Procedures

All requests or applications for services to be provided by the Independent Auditors that do not require specific approval by the Audit Committee will be submitted to the Fund’s Principal Financial and Accounting Officer and must include a detailed description of the services to be rendered. The Fund’s Principal Financial and Accounting Officer will determine whether such services are included within the list of services that have received the general pre-approval of the Audit Committee. The Audit Committee will be informed on a timely basis of any such services rendered by the Independent Auditors. Requests or applications to provide services that require specific approval by the Audit Committee or Chairperson of the Audit Committee will be submitted to the Audit Committee by the Fund's Principal Financial and Accounting Officer, who, after consultation with the Independent Auditors, will discuss whether, the request or application is consistent with the SEC’s rules on auditor independence.

The Audit Committee has designated the Fund’s Principal Financial and Accounting Officer to monitor the performance of all services provided by the Independent Auditors and to determine whether such services are in compliance with this Policy. The Fund’s Principal Financial and Accounting Officer will report to the Audit Committee on a periodic basis on the results of its monitoring. Both the Fund’s Principal Financial and Accounting Officer and management will immediately report to the Chairperson of the Audit Committee any breach of this Policy that comes to the attention of the Fund’s Principal Financial and Accounting Officer or any member of management.

9. Additional Requirements

The Audit Committee has determined to take additional measures on an annual basis to meet its responsibility to oversee the work of the Independent Auditors and to assure the auditor’s independence from the Fund, such as reviewing a formal written statement from the Independent Auditors delineating all relationships between the Independent Auditors and the Fund, consistent with the PCAOB’s Ethics and Independence Rule 3526, and discussing with the Independent Auditors its methods and procedures for ensuring independence.

10. Covered Entities

Covered Entities include the Fund’s investment adviser(s) and any entity controlling, controlled by or under common control with the Fund’s investment adviser(s) that provides ongoing services to the Fund(s). Beginning with non-audit service contracts entered into on or after May 6, 2003, the Fund’s audit committee must pre-approve non-audit services provided not only to the Fund but also to the Covered Entities if the engagements relate directly to the operations and financial reporting of the Fund. This list of Covered Entities would include:

Morgan Stanley Funds

Morgan Stanley & Co. LLC

Morgan Stanley Investment Management Inc.

Morgan Stanley Investment Management Limited

Morgan Stanley Investment Management Private Limited

Morgan Stanley Asset & Investment Trust Management Co., Limited

Morgan Stanley Investment Management Company

Morgan Stanley Services Company, Inc.

Morgan Stanley Distribution, Inc.

Morgan Stanley AIP GP LP

Morgan Stanley Alternative Investment Partners LP

Morgan Stanley Smith Barney LLC

Morgan Stanley Capital Management LLC

Morgan Stanley Asia Limited

Morgan Stanley Services Group

(e)(2) Beginning with non-audit service contracts entered into on or after May 6, 2003, the audit committee also is required to pre-approve services to Covered Entities to the extent that the services are determined to have a direct impact on the operations or financial reporting of the Registrant. 100% of such services were pre-approved by the audit committee pursuant to the Audit Committee’s pre-approval policies and procedures (attached hereto).

(f) Not applicable.

(g) See table above.

(h) The audit committee of the Board of Trustees has considered whether the provision of services other than audit services performed by the auditors to the Registrant and Covered Entities is compatible with maintaining the auditors' independence in performing audit services.

APPENDIX A

Pre-Approved Audit Services

Service  Range of Fees
	The Fund(s)	Covered Entities
Statutory audits or financial audits for the Funds	For a complete list of fees, please contact the legal department **	N/A
Services associated with SEC registration statements (including new fund filings/seed audits), periodic reports and other documents filed with the SEC or other documents issued in connection with securities offerings (e.g., comfort letters for closed-end fund offerings, consents), and assistance in responding to SEC comment letters	*	*
Consultations by the Fund’s management as to the accounting or disclosure treatment of transactions or events and/or the actual or potential impact of final or proposed rules, standards or interpretations by the SEC, FASB, or other regulatory or standard setting bodies (Note: Under SEC rules, some consultations may be “audit related” services rather than “audit” services)	*	*

Pre-Approved Audit-Related Services

Service  Range of Fees
	The Fund(s)	Covered Entities
Attest procedures not required by statute or regulation	*	*
Due diligence services pertaining to potential fund mergers	*	*
Consultations by the Fund’s management as to the accounting or disclosure treatment of transactions or events and/or the actual or potential impact of final or proposed rules, standards or interpretations by the SEC, FASB, or other regulatory or standard-setting bodies (Note: Under SEC rules, some consultations may be “audit” services rather than “audit-related” services)	*	*
General assistance with implementation of the requirements of SEC rules or listing standards promulgated pursuant to the Sarbanes-Oxley Act	*	*

Pre-Approved Tax Services

Service   Range of Fees
	The Fund(s)	Covered Entities
U.S. federal, state and local tax planning and advice	*	*
U.S. federal, state and local tax compliance	*	*
International tax planning and advice	*	*
International tax compliance	*	*
Review/preparation of federal, state, local and international income, franchise, and other tax returns	$400,000 PwC	N/A
Identification of Passive Foreign Investment Companies PwC ITV Tool – assist in determining which Fund holdings have foreign capital gains tax exposure	$150,000 PwC $125,000 PwC	* *
Foreign Tax Services - Preparation of local foreign tax returns and assistance with local tax compliance issues (including maintenance of transaction schedules, assistance in periodic tax remittances, tax registration, representing funds before foreign revenue authorities and assistance with assessment orders)	$500,000 PwC/EY	*
Assistance with tax audits and appeals before the IRS and similar state, local and foreign agencies	*	*
Tax advice and assistance regarding statutory, regulatory or administrative developments (e.g., excise tax reviews, evaluation of Fund’s tax compliance function)	*	*

Pre-Approved All Other Services

Service Range of Fees
	The Fund(s)	Covered Entities
Risk management advisory services, e.g., assessment and testing of security infrastructure controls	*	*

*Aggregate fees related to the pre-approved services will be limited to 10% of the 2020/2021 annual fees for audit and tax services (see fee schedule distributed by the Auditors).

** Audit and tax services for new funds/portfolios will be subject to the maximum audit and tax fee for a fund/portfolio on fee schedule distributed by the Auditors.

Prohibited Non-Audit Services

· Bookkeeping or other services related to the accounting records or financial statements of the audit client

· Financial information systems design and implementation

· Appraisal or valuation services, fairness opinions or contribution-in-kind reports

· Actuarial services

· Internal audit outsourcing services

· Management functions

· Human resources

· Broker-dealer, investment adviser or investment banking services

· Legal services

· Expert services unrelated to the audit

Item 5. Audit Committee of Listed Registrants.

(a) The registrant has a separately-designated standing audit committee established in accordance with Section 3(a)(58)(A) of the Exchange Act whose members are:

Joseph J. Kearns, Jakki L. Haussler, Michael F. Klein and W. Allen Reed.

(b) Not applicable.

Item 6. Schedule of Investments

(a) Refer to Item 1.

(b) Not applicable.

Item 7. Disclosure of Proxy Voting Policies and Procedures for Closed-End Management Investment Companies.

Applicable only to reports filed by closed-end funds.

Item 8. Portfolio Managers of Closed-End Management Investment Companies

Applicable only to reports filed by closed-end funds.

Item 9. Closed-End Fund Repurchases

Applicable only to reports filed by closed-end funds.

Item 10. Submission of Matters to a Vote of Security Holders

There have been no material changes to the procedures by which shareholders may recommend nominee to the Fund’s Board of Trustees since the Fund last provided disclosure in response to this item.

Item 11. Controls and Procedures

(a) The registrant’s principal executive officer and principal financial officer have concluded that the registrant’s disclosure controls and procedures are sufficient to ensure that information required to be disclosed by the registrant in this Form N-CSR was recorded, processed, summarized and reported within the time periods specified in the Securities and Exchange Commission's rules and forms, based upon such officers' evaluation of these controls and procedures as of a date within 90 days of the filing date of the report.

(b) There were no changes in the registrant's internal control over financial reporting that occurred during the second fiscal quarter of the period covered by this report that has materially affected, or is reasonably likely to materially affect, the registrant's internal control over financial reporting.

Item 12. Disclosure of Securities Lending Activities for Closed End Management Investment Companies.

Not Applicable

Item 13. Exhibits

(a) The Code of Ethics for Principal Executive and Senior Financial Officers.

(b) A separate certification for each principal executive officer and principal financial officer of the registrant as part of EX-99.CERT.

SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934 and the Investment Company Act of 1940, the registrant has duly caused this report to be signed on its behalf by the undersigned, thereunto duly authorized.

Morgan Stanley Institutional Fund Trust

/s/ John H. Gernon

John H. Gernon

Principal Executive Officer

November 17, 2020

Pursuant to the requirements of the Securities Exchange Act of 1934 and the Investment Company Act of 1940, this report has been signed by the following persons on behalf of the registrant and in the capacities and on the dates indicated.

/s/ John H. Gernon

John H. Gernon

Principal Executive Officer

November 17, 2020

/s/ Francis Smith

Francis Smith

Principal Financial Officer

November 17, 2020