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

    <schemaVersion>X0609</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2026-09-01</periodOfReport>

    <issuer>
        <issuerCik>0002100782</issuerCik>
        <issuerName>Generate Biomedicines, Inc.</issuerName>
        <issuerTradingSymbol>GENB</issuerTradingSymbol>
        <issuerForeignTradingSymbol></issuerForeignTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001665419</rptOwnerCik>
            <rptOwnerName>ARNOLD FRANCES</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerNonUSAddressFlag>false</rptOwnerNonUSAddressFlag>
            <rptOwnerStreet1>GENERATE BIOMEDICINES, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>101 SOUTH STREET, SUITE 900</rptOwnerStreet2>
            <rptOwnerCity>SOMERVILLE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02143</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>true</isDirector>
            <isOfficer>false</isOfficer>
            <isTenPercentOwner>false</isTenPercentOwner>
            <isOther>false</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <aff10b5One>true</aff10b5One>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2026-09-01</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
                <equitySwapInvolved>false</equitySwapInvolved>
                <footnoteId id="F1"/>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>1000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>16.002</value>
                    <footnoteId id="F2"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>231472</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>232472</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By The Frances Arnold 2010 Irrevocable Trust</value>
                    <footnoteId id="F3"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">These transactions were effected by the Reporting Person pursuant to a Rule 10b5-1 trading plan adopted by the Reporting Person on March 13, 2026.</footnote>
        <footnote id="F2">The price reported in Column 4 is a weighted average price. The shares were sold in multiple transactions at prices ranging from $16.00 to $16.01 per share, inclusive. The Reporting Person undertakes to provide to the Issuer, any security holder of the Issuer, or the staff of the Securities and Exchange Commission, upon request, full information regarding the number of shares sold at each separate price within the range set forth in this footnote.</footnote>
        <footnote id="F3">The Reporting Person disclaims beneficial ownership of such shares for purposes of Section 16 of the Securities Exchange Act of 1934, as amended (the &quot;Exchange Act&quot;), except to the extent of her pecuniary interest therein, if any. This report shall not be deemed an admission that she is a beneficial owner of such shares for the purpose of Section 16 of the Exchange Act, or for any other purpose.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>/s/ Michael Wolf, Attorney-in-Fact</signatureName>
        <signatureDate>2026-09-03</signatureDate>
    </ownerSignature>
</ownershipDocument>
