Executive Chair Letter Agreement between the Company and Graham Cooper, dated January 27, 2022

Exhibit 10.1

450 East Jamie Court

South San Francisco, CA 94080

January 25, 2022

Graham Cooper

Dear Graham,

This Letter of Agreement (this “Agreement”) confirms your appointment as Executive Chairman of Applied Molecular Transport Inc. (the “Company”) and your continued service as a member of the Company’s Board of Directors (the “Board”). Your appointment as Executive Chairman of the Company is subject to approval by the Board. This Agreement sets out the duties, terms of appointment and remuneration of the Executive Chairman position. By accepting the appointment, you confirm that you are not subject to any restrictions or non-compete agreements which prevent you from holding office as an executive officer of the Company.

Your duties as Executive Chairman shall include the following:

Graham Cooper

January 25, 2022

Page 2

Subject to the Board’s approval of the terms of this Agreement, your appointment as Executive Chairman is at-will. Accordingly, you may terminate your position as Executive Chairman with the Company at any time and for any reason whatsoever simply by notifying the Board. Likewise, the Board may terminate your appointment as Executive Chairman at any time and for any reason, with or without cause or advance notice.

You shall continue to serve as a non-independent member of the Board for the remainder of your current term and until your successor shall have been duly elected and qualified.

Graham Cooper

January 25, 2022

Page 3

If your employment with the Company is terminated by the Company without “Cause” (excluding by reason of your death or “Disability”) or by you as a result of a “Constructive Termination”, in either case, within the “Change in Control Period”, 100% of your then-unvested Company equity awards that you receive during the course of your employment with the Company will fully vest and become exercisable, subject to and effective upon you signing and not revoking a release of claims in a form provided by the Company within 60 days following your termination date. For the avoidance of doubt, your Company equity awards that are outstanding prior to the date of this letter will be subject to vesting acceleration in accordance with their existing terms.

If, in connection with a “Change in Control,” you have or could receive payments or benefits (the “Payments”) that would constitute “parachute payments” within the meaning of Section 280G of the Internal Revenue Code of 1986, as amended (the “Code”) and otherwise would be subject to the excise tax imposed by Section 4999 of the Code, then the Payments will be subject to terms and conditions that are at least as favorable as those terms and conditions applicable to the Company’s other senior executive officers in connection with such Change in Control. Capitalized terms used in this Section 3(d) will have the meaning ascribed to them in the Company’s Senior Executive Change in Control and Severance Policy as in effect as of the date hereof, unless otherwise specifically defined in this Agreement.

It is accepted and acknowledged that you have business interests other than those of the Company and have declared any conflicts that are apparent at present. If you become aware of any potential conflicts of interest, you shall immediately disclose such conflicts to the Company’s CEO and General Counsel. In addition, as the Executive Chairman you acknowledge that you will be subject to the Company’s more restrictive conflict of interest restrictions under the Company’s Code of Business Conduct which will prohibit you from performing services as a director, advisor, employee, agent or contractor for a customer, a supplier or any other entity that has a business relationship with the Company or is a competitor, or may be deemed a competitor, without approval from the Company.

Graham Cooper

January 25, 2022

Page 4

As a condition of your employment, you will be required to abide by the Company’s policies and procedures and execute and abide by the Company’s At-Will Employment, Confidential Information, Invention Assignment, and Arbitration Agreement (“Confidentiality Agreement”). In your work for the Company, you will be expected to not make any unauthorized use of, or disclose, the confidential information or materials, including trade secrets, of any former employer or other third party to whom you owe an obligation of confidentiality. Rather, you will be expected to use only that information generally known and used by persons with training and experience comparable to your own, which information is common knowledge in the industry or otherwise legally available in the public domain, or which is otherwise provided or developed by the Company. By signing below, you are representing to us that you will be able to perform your duties within the guidelines described in this paragraph. You represent further that you have disclosed to the Company any contract you have signed or other relationship that you have, in each case, that may restrict your activities on behalf of the Company in any manner as set forth in this Agreement.

This Agreement, together with your Confidentiality Agreement and any plans or agreements governing any outstanding stock options granted or to be granted to you by the Company under its equity plans and the applicable stock option agreement thereunder, form the complete and exclusive statement of your agreement with the Company concerning this offer, and supersede any other representations or promises made to you by any party, whether oral or written. The terms of the Agreement cannot be changed other than by a written agreement signed by you and a duly authorized officer of the Company. This Agreement is to be governed by the laws of the state of California without reference to its conflicts of law principles. In case any provision contained in this Agreement shall, for any reason, be held invalid or unenforceable in any respect, such invalidity or unenforceability will not affect the other provisions of this Agreement, and such provision will be construed and enforced so as to render it valid and enforceable consistent with the general intent of the parties insofar as possible under applicable law. With respect to the enforcement of this Agreement, no waiver of any right hereunder will be effective unless it is in writing.

This Agreement may be executed in more than one counterpart, and signatures transmitted electronically will be deemed equivalent to originals.

[Signature Page follows]

Graham Cooper

January 25, 2022

Page 5

Please signify your acceptance of the terms of this Agreement by signing and returning to me the enclosed duplicate copy of this Agreement.