Applied Molecular Transport (AMTI) S-3ASR Automatic shelf registration

Exhibit 23.1

CONSENT OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM

We consent to the incorporation by reference in this Registration Statement on Form S-3 of our report dated March 19, 2021, relating to the financial statements of Applied Molecular Transport Inc., appearing in the Annual Report on Form 10-K of Applied Molecular Transport Inc. for the year ended December 31, 2020. We also consent to the reference to us under the heading “Experts” in such Registration Statement.

/s/ Deloitte & Touche LLP

San Francisco, California

July 1, 2021