<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0508</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2025-09-05</periodOfReport>

    <issuer>
        <issuerCik>0001785279</issuerCik>
        <issuerName>Metagenomi, Inc.</issuerName>
        <issuerTradingSymbol>MGX</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0002009713</rptOwnerCik>
            <rptOwnerName>Wein Matthew</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O METAGENOMI, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>5959 HORTON STREET, 7TH FLOOR</rptOwnerStreet2>
            <rptOwnerCity>EMERYVILLE</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94608</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>false</isDirector>
            <isOfficer>true</isOfficer>
            <isTenPercentOwner>false</isTenPercentOwner>
            <isOther>false</isOther>
            <officerTitle>See Remarks</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <aff10b5One>false</aff10b5One>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2025-09-05</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
                <equitySwapInvolved>false</equitySwapInvolved>
                <footnoteId id="F1"/>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>199</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>1.81</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>19230</value>
                    <footnoteId id="F2"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2025-12-01</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>false</equitySwapInvolved>
                <footnoteId id="F3"/>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>96000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>1.60</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>115230</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">These shares of common stock were automatically sold for the purpose of satisfying the Reporting Person's tax withholding obligations upon the vesting of certain restricted stock units (&quot;RSUs&quot;) granted to the Reporting Person on April 1, 2024, and does not represent a volitional trade by the Reporting Person.</footnote>
        <footnote id="F2">Includes 1,359 shares acquired under the Company's employee stock purchase plan (&quot;ESPP&quot;) on May 30, 2025 and 1,377 shares acquired under the Company's ESPP on November 28, 2025.</footnote>
        <footnote id="F3">These shares represent RSUs. 50% of the RSUs shall vest on December 5, 2026, with the remainder vesting on December 5, 2027, subject to the Reporting Person's continued service with the Issuer on each such vesting date.</footnote>
    </footnotes>

    <remarks>Title: General Counsel, Compliance Officer and Corporate Secretary</remarks>

    <ownerSignature>
        <signatureName>/s/ Matthew L. Wein</signatureName>
        <signatureDate>2025-12-01</signatureDate>
    </ownerSignature>
</ownershipDocument>
