Noninterest expense was $11.2 million for the three months ended September 30, 2021 compared with $11.9 million for the comparable period a year earlier. Excluding the prepayment penalty of $2.5 million taken in 2020 as part of a deleverage strategy, noninterest expense increased $1.8 million in 2021 compared to 2020.
In fiscal 2021, noninterest expense was $41.8 million compared with $40.6 million in fiscal 2020. Excluding prepayment penalties, noninterest expense increased $3.5 million in 2021 compared to 2020 primarily reflecting increases in compensation and employee benefits expenses and other operating expenses. In both the quarterly and year to date periods of 2021, increased compensation and employee benefits included performance-based commissions paid to residential mortgage team members, reflecting strong mortgage origination activity.
Balance Sheet, Asset Quality and Capital Adequacy Review
Total assets were $1.86 billion at September 30, 2021 compared with $1.89 billion at September 30, 2020, primarily due to decreases in loans receivable, regulatory stock and bank-owned life insurance offset in part by increased investment securities available for sale and investment securities held to maturity. The Company built the majority of its cash position in the fiscal second quarter of 2020 and has maintained that position through the fourth quarter of fiscal 2021 as managed declines in borrowed funds were more than offset by increases in deposits. At September 30, 2021, cash and cash equivalents were $158.9 million.
Total net loans were $1.34 billion at September 30, 2021 compared with $1.42 billion at September 30, 2020. Residential real estate loans were $580.3 million at September 30, 2021 compared to $610.2 million at September 30, 2020. The Company sold $67.5 million in residential mortgage loans to the Federal Home Loan Bank of Pittsburgh during the twelve months ended September 30, 2021, recording gains on the sale of these loans in noninterest income. Indirect auto loans declined by $25.9 million during the twelve months ended September 30, 2021, reflecting expected runoff of the portfolio as the Company exits the indirect auto lending business.
Commercial real estate loans were $591.1 million at September 30, 2021 compared with $509.6 million at September 30, 2020. Commercial loans were $63.5 million, compared with $139.6 million at September 30, 2020. The decline included a net decrease of $54.1 million in PPP loans during fiscal 2021.
Loans remaining in forbearance at September 30, 2021 included $30.6 million in commercial real estate, $374,000 in commercial and $140,000 in mortgage. In total, these loans represent 2.3% of total outstanding loans at September 30, 2021 compared to 4.5% at September 30, 2020 and 12.4% at June 30, 2020.
Total deposits were $1.64 billion at September 30, 2021, up 6.0% compared with $1.54 billion at September 30, 2020. Core deposits (demand, savings and money market accounts) were $1.43 billion, or 87.2% of total deposits, at September 30, 2021. Noninterest bearing demand accounts were $257.7 million, up 6.2% from September 30, 2020, interest bearing demand accounts rose 100.6% to $551.2 million from September 30, 2020 levels, and money market accounts were $428.3 million, up $26.4 million or 6.6% from September 30, 2020. Total borrowings decreased to zero at September 30, 2021 from $125.9 million at September 30, 2020 as the Company shifted its wholesale funding to lower costing brokered deposits.
Nonperforming assets were $16.3 million, or 0.88% of total assets, at September 30, 2021, compared with $21.9 million, or 1.20% of total assets at June 30, 2021, and $20.6 million, or 1.09% of total assets, at September 30, 2020. Two commercial real estate loans account for just over 50% of the nonperforming assets at September 30, 2021. Management is confident that these loans are adequately collateralized.