Metagenomi Therapeutics, Inc.

To Be Held on June 10, 2025

The Board of Directors of Metagenomi, Inc. (the “Board of Directors,” “Board,” or “our Board”) is soliciting proxies from stockholders for its use at the 2025 annual meeting of our stockholders (the “Annual Meeting”), and at any continuation, postponement, or adjournment of that meeting. The Annual Meeting is scheduled to be held on June 10, 2025, at 8:00 a.m., Pacific Time, in a virtual meeting format, which will be conducted via live webcast atwww.virtualshareholdermeeting.com/MGX2025.

In this proxy statement, “we,” “our,” “us,” the “Company,” and “Metagenomi” refer to Metagenomi, Inc.

On or about April 28, 2025, we will commence sending the Notice of Internet Availability of Proxy Materials (the “Notice”) to all stockholders of record entitled to notice of, and to vote at, the Annual Meeting.

IMPORTANT NOTICE REGARDING THE AVAILABILITY OF PROXY MATERIALS FOR THE 2025 ANNUAL STOCKHOLDER MEETING TO BE HELD ON June 10, 2025.

This proxy statement, the accompanying proxy card and our annual report to stockholders for the fiscal year ended December 31, 2024, which includes our audited financial statements, are available for viewing, printing and downloading atwww.proxyvote.com. To view these materials, please have your 16-digit control number available that appears on your Notice or proxy card. On this website, you can also elect to receive distributions of our proxy statements and annual reports to stockholders for future annual meetings by electronic delivery. For specific instructions on making such an election, please refer to the instructions on your proxy card or voting instruction form.

Additionally, you can find a copy of our Annual Report on Form 10-K for the fiscal year ended December 31, 2024 (“2024 Annual Report”), as filed with the Securities and Exchange Commission (the “SEC”) on the SEC’s website atwww.sec.gov, or in the “Financials and Filings” tab of the “Investors” section of our website athttps://metagenomi.co/. You may also obtain a printed copy of our 2024 Annual Report, including our financial statements, except for the exhibits, free of charge, from us by following the instructions included on the Notice or by sending a written request to: Metagenomi, Inc., 5959 Horton Street, 7th Floor, Emeryville, CA 94608, Attention: Secretary.