<?xml version="1.0" encoding="US-ASCII"?>
<!-- DFIN New ActiveDisclosure (SM) XBRL Schema Document - http://www.dfinsolutions.com/ -->
<!-- Creation Date :2023-08-09T15:07:32.4618+00:00 -->
<!-- Copyright (c) 2023 Donnelly Financial Solutions, Inc. All Rights Reserved. -->
<xsd:schema targetNamespace="http://www.synlogictx.com/20230630" attributeFormDefault="unqualified" elementFormDefault="qualified" xmlns:dtr-types="http://www.xbrl.org/dtr/type/2022-03-31" xmlns:enum2="http://xbrl.org/2020/extensible-enumerations-2.0" xmlns:srt="http://fasb.org/srt/2023" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:link="http://www.xbrl.org/2003/linkbase" xmlns:us-gaap="http://fasb.org/us-gaap/2023" xmlns:dei="http://xbrl.sec.gov/dei/2023" xmlns:sybx="http://www.synlogictx.com/20230630" xmlns:xbrldt="http://xbrl.org/2005/xbrldt" xmlns:xbrli="http://www.xbrl.org/2003/instance" xmlns:xlink="http://www.w3.org/1999/xlink">
  <xsd:import schemaLocation="http://www.xbrl.org/2003/xbrl-instance-2003-12-31.xsd" namespace="http://www.xbrl.org/2003/instance"/>
  <xsd:import schemaLocation="http://www.xbrl.org/2003/xbrl-linkbase-2003-12-31.xsd" namespace="http://www.xbrl.org/2003/linkbase"/>
  <xsd:import schemaLocation="http://www.xbrl.org/2005/xbrldt-2005.xsd" namespace="http://xbrl.org/2005/xbrldt"/>
  <xsd:import schemaLocation="https://xbrl.sec.gov/dei/2023/dei-2023.xsd" namespace="http://xbrl.sec.gov/dei/2023"/>
  <xsd:import schemaLocation="https://www.xbrl.org/dtr/type/2022-03-31/types.xsd" namespace="http://www.xbrl.org/dtr/type/2022-03-31"/>
  <xsd:import schemaLocation="https://xbrl.fasb.org/us-gaap/2023/elts/us-gaap-2023.xsd" namespace="http://fasb.org/us-gaap/2023"/>
  <xsd:import schemaLocation="https://xbrl.fasb.org/srt/2023/elts/srt-2023.xsd" namespace="http://fasb.org/srt/2023"/>
  <xsd:annotation>
    <xsd:appinfo>
      <link:linkbaseRef xlink:arcrole="http://www.w3.org/1999/xlink/properties/linkbase" xlink:href="sybx-20230630_lab.xml" xlink:role="http://www.xbrl.org/2003/role/labelLinkbaseRef" xlink:title="Labels link" xlink:type="simple"/>
      <link:linkbaseRef xlink:arcrole="http://www.w3.org/1999/xlink/properties/linkbase" xlink:href="sybx-20230630_pre.xml" xlink:role="http://www.xbrl.org/2003/role/presentationLinkbaseRef" xlink:title="Presentation link" xlink:type="simple"/>
      <link:linkbaseRef xlink:arcrole="http://www.w3.org/1999/xlink/properties/linkbase" xlink:href="sybx-20230630_def.xml" xlink:role="http://www.xbrl.org/2003/role/definitionLinkbaseRef" xlink:title="Definition link" xlink:type="simple"/>
      <link:linkbaseRef xlink:arcrole="http://www.w3.org/1999/xlink/properties/linkbase" xlink:href="sybx-20230630_cal.xml" xlink:role="http://www.xbrl.org/2003/role/calculationLinkbaseRef" xlink:title="Calculation link" xlink:type="simple"/>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/Role_DocumentDocumentAndEntityInformation" id="Role_DocumentDocumentAndEntityInformation">
        <link:definition>100000 - Document - Document and Entity Information</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/Role_StatementConsolidatedBalanceSheetsUnaudited" id="Role_StatementConsolidatedBalanceSheetsUnaudited">
        <link:definition>100010 - Statement - Consolidated Balance Sheets (Unaudited)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/Role_StatementConsolidatedBalanceSheetsUnauditedParenthetical" id="Role_StatementConsolidatedBalanceSheetsUnauditedParenthetical">
        <link:definition>100020 - Statement - Consolidated Balance Sheets (Unaudited) (Parenthetical)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/Role_StatementConsolidatedStatementsOfOperationsAndComprehensiveLossUnaudited" id="Role_StatementConsolidatedStatementsOfOperationsAndComprehensiveLossUnaudited">
        <link:definition>100030 - Statement - Consolidated Statements of Operations and Comprehensive Loss (Unaudited)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/Role_StatementConsolidatedStatementsOfStockholdersEquityUnaudited" id="Role_StatementConsolidatedStatementsOfStockholdersEquityUnaudited">
        <link:definition>100040 - Statement - Consolidated Statements of Stockholders' Equity (Unaudited)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/Role_StatementConsolidatedStatementsOfCashFlowsUnaudited" id="Role_StatementConsolidatedStatementsOfCashFlowsUnaudited">
        <link:definition>100050 - Statement - Consolidated Statements of Cash Flows (Unaudited)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/Role_DisclosureNatureOfBusiness" id="Role_DisclosureNatureOfBusiness">
        <link:definition>100060 - Disclosure - Nature of Business</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/Role_DisclosureSummaryOfSignificantAccountingPolicies" id="Role_DisclosureSummaryOfSignificantAccountingPolicies">
        <link:definition>100070 - Disclosure - Summary of Significant Accounting Policies</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/Role_DisclosureFairValueOfFinancialInstruments" id="Role_DisclosureFairValueOfFinancialInstruments">
        <link:definition>100080 - Disclosure - Fair Value of Financial Instruments</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/DisclosureAvailableforsaleSecurities" id="DisclosureAvailableforsaleSecurities">
        <link:definition>100090 - Disclosure - Available-for-Sale Securities</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/Role_DisclosurePropertyAndEquipmentNet" id="Role_DisclosurePropertyAndEquipmentNet">
        <link:definition>100100 - Disclosure - Property and Equipment, Net</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/Role_DisclosureAccruedExpenses" id="Role_DisclosureAccruedExpenses">
        <link:definition>100110 - Disclosure - Accrued Expenses</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/Role_DisclosureStockholdersEquity" id="Role_DisclosureStockholdersEquity">
        <link:definition>100120 - Disclosure - Stockholders' Equity</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/DisclosureEquityBasedCompensation1" id="DisclosureEquityBasedCompensation1">
        <link:definition>100130 - Disclosure - Equity based Compensation</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/Role_DisclosureCollaborationAgreements" id="Role_DisclosureCollaborationAgreements">
        <link:definition>100140 - Disclosure - Collaboration Agreements</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/Role_DisclosureNetLossPerShare" id="Role_DisclosureNetLossPerShare">
        <link:definition>100150 - Disclosure - Net Loss per Share</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/DisclosureShareRepurchase" id="DisclosureShareRepurchase">
        <link:definition>100160 - Disclosure - Share Repurchase</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/Role_DisclosureCommitmentsAndContingencies" id="Role_DisclosureCommitmentsAndContingencies">
        <link:definition>100170 - Disclosure - Commitments and Contingencies</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/Role_DisclosureRelatedPartyTransactions" id="Role_DisclosureRelatedPartyTransactions">
        <link:definition>100180 - Disclosure - Related-Party Transactions</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/Role_DisclosureSummaryOfSignificantAccountingPoliciesPolicies" id="Role_DisclosureSummaryOfSignificantAccountingPoliciesPolicies">
        <link:definition>100190 - Disclosure - Summary of Significant Accounting Policies (Policies)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/Role_DisclosureFairValueOfFinancialInstrumentsTables" id="Role_DisclosureFairValueOfFinancialInstrumentsTables">
        <link:definition>100200 - Disclosure - Fair Value of Financial Instruments (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/DisclosureAvailableforsaleSecuritiesTables" id="DisclosureAvailableforsaleSecuritiesTables">
        <link:definition>100210 - Disclosure - Available-for-Sale Securities (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/Role_DisclosurePropertyAndEquipmentNetTables" id="Role_DisclosurePropertyAndEquipmentNetTables">
        <link:definition>100220 - Disclosure - Property and Equipment, Net (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/Role_DisclosureAccruedExpensesTables" id="Role_DisclosureAccruedExpensesTables">
        <link:definition>100230 - Disclosure - Accrued Expenses (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/Role_DisclosureStockholdersEquityTables" id="Role_DisclosureStockholdersEquityTables">
        <link:definition>100240 - Disclosure - Stockholders' Equity (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/DisclosureEquityBasedCompensationTables" id="DisclosureEquityBasedCompensationTables">
        <link:definition>100250 - Disclosure - Equity based Compensation (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/Role_DisclosureNetLossPerShareTables" id="Role_DisclosureNetLossPerShareTables">
        <link:definition>100260 - Disclosure - Net Loss per Share (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/Role_DisclosureNatureOfBusinessAdditionalInformationDetail" id="Role_DisclosureNatureOfBusinessAdditionalInformationDetail">
        <link:definition>100270 - Disclosure - Nature of Business - Additional Information (Detail)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/Role_DisclosureFairValueOfFinancialInstrumentsScheduleOfCompanySClassifiedAssetsMeasuredAtFairValueOnRecurringBasisDetail" id="Role_DisclosureFairValueOfFinancialInstrumentsScheduleOfCompanySClassifiedAssetsMeasuredAtFairValueOnRecurringBasisDetail">
        <link:definition>100280 - Disclosure - Fair Value of Financial Instruments - Schedule of Company's Classified Assets Measured at Fair Value on Recurring Basis (Detail)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/DisclosureFairValueOfFinancialInstrumentsScheduleOfAssetsMeasuredAtFairValueAndTheGrossUnrealizedHoldingGainsAndLossesDetails" id="DisclosureFairValueOfFinancialInstrumentsScheduleOfAssetsMeasuredAtFairValueAndTheGrossUnrealizedHoldingGainsAndLossesDetails">
        <link:definition>100290 - Disclosure - Fair Value of Financial Instruments - Schedule of Assets measured at fair value and the gross unrealized holding gains and losses (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/DisclosureAvailableforsaleSecuritiesSummaryOfAvailableforsaleSecuritiesHeldDetail" id="DisclosureAvailableforsaleSecuritiesSummaryOfAvailableforsaleSecuritiesHeldDetail">
        <link:definition>100300 - Disclosure - Available-for-Sale Securities - Summary of Available-for-Sale Securities Held (Detail)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/DisclosureAvailableforsaleSecuritiesAdditionalInformationDetail" id="DisclosureAvailableforsaleSecuritiesAdditionalInformationDetail">
        <link:definition>100310 - Disclosure - Available-for-Sale Securities - Additional Information (Detail)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/Role_DisclosurePropertyAndEquipmentNetScheduleOfPropertyAndEquipmentNetDetail" id="Role_DisclosurePropertyAndEquipmentNetScheduleOfPropertyAndEquipmentNetDetail">
        <link:definition>100320 - Disclosure - Property and Equipment, Net - Schedule of Property and Equipment, Net (Detail)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/Role_DisclosureAccruedExpensesScheduleOfAccruedExpensesDetail" id="Role_DisclosureAccruedExpensesScheduleOfAccruedExpensesDetail">
        <link:definition>100330 - Disclosure - Accrued Expenses - Schedule of Accrued Expenses (Detail)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/Role_DisclosureStockholdersEquityAdditionalInformationDetail" id="Role_DisclosureStockholdersEquityAdditionalInformationDetail">
        <link:definition>100340 - Disclosure - Stockholders Equity - Additional Information (Detail)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/Role_DisclosureStockholdersEquityScheduleOfSharesOfCommonStockReservedForFutureIssuanceDetail" id="Role_DisclosureStockholdersEquityScheduleOfSharesOfCommonStockReservedForFutureIssuanceDetail">
        <link:definition>100350 - Disclosure - Stockholders Equity - Schedule of Shares of Common Stock Reserved for Future Issuance (Detail)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/DisclosureEquityBasedCompensationAdditionalInformationDetail" id="DisclosureEquityBasedCompensationAdditionalInformationDetail">
        <link:definition>100360 - Disclosure - Equity based Compensation - Additional Information (Detail)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/DisclosureEquityBasedCompensationScheduleOfEquitybasedCompensationExpensesDetail" id="DisclosureEquityBasedCompensationScheduleOfEquitybasedCompensationExpensesDetail">
        <link:definition>100370 - Disclosure - Equity based Compensation - Schedule of Equity-based Compensation Expenses (Detail)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/DisclosureEquityBasedCompensationScheduleOfEquitybasedCompensationExpensesByAwardTypeDetail" id="DisclosureEquityBasedCompensationScheduleOfEquitybasedCompensationExpensesByAwardTypeDetail">
        <link:definition>100380 - Disclosure - Equity based Compensation - Schedule of Equity-based Compensation Expenses by Award Type (Detail)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/Role_DisclosureCollaborationAgreementsAdditionalInformationDetail" id="Role_DisclosureCollaborationAgreementsAdditionalInformationDetail">
        <link:definition>100390 - Disclosure - Collaboration Agreements - Additional Information (Detail)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/Role_DisclosureNetLossPerShareAdditionalInformationDetail" id="Role_DisclosureNetLossPerShareAdditionalInformationDetail">
        <link:definition>100400 - Disclosure - Net Loss per Share - Additional Information (Detail)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/Role_DisclosureNetLossPerShareScheduleOfPotentiallyCommonSharesExcludedFromCalculationOfNetLossPerShareDetail" id="Role_DisclosureNetLossPerShareScheduleOfPotentiallyCommonSharesExcludedFromCalculationOfNetLossPerShareDetail">
        <link:definition>100410 - Disclosure - Net Loss per Share - Schedule of Potentially Common Shares Excluded from Calculation of Net Loss Per share (Detail)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/DisclosureShareRepurchaseAdditionalInformationDetails" id="DisclosureShareRepurchaseAdditionalInformationDetails">
        <link:definition>100420 - Disclosure - Share Repurchase (Additional Information) (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/Role_DisclosureCommitmentsAndContingenciesAdditionalInformationDetail" id="Role_DisclosureCommitmentsAndContingenciesAdditionalInformationDetail">
        <link:definition>100430 - Disclosure - Commitments and Contingencies - Additional Information (Detail)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.synlogictx.com/20230630/taxonomy/role/Role_DisclosureRelatedPartyTransactionsAdditionalInformationDetail" id="Role_DisclosureRelatedPartyTransactionsAdditionalInformationDetail">
        <link:definition>100440 - Disclosure - Related-Party Transactions - Additional Information (Detail)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
    </xsd:appinfo>
  </xsd:annotation>
  <xsd:element id="sybx_CurrentLiabilitiesMember" name="CurrentLiabilitiesMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="sybx_AtTheMarketMember" name="AtTheMarketMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="sybx_ScheduleOfSharesOfCommonStockReservedForFutureIssuanceTableTextBlock" name="ScheduleOfSharesOfCommonStockReservedForFutureIssuanceTableTextBlock" type="dtr-types:textBlockItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false"/>
  <xsd:element id="sybx_PrepaidResearchAndDevelopmentNoncurrent" name="PrepaidResearchAndDevelopmentNoncurrent" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="sybx_ProceedsFromIssuanceOfCommonStockAndPreFundedWarrants" name="ProceedsFromIssuanceOfCommonStockAndPreFundedWarrants" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="sybx_PrepaymentToRelatedPartyForCollaborationAgreement" name="PrepaymentToRelatedPartyForCollaborationAgreement" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit"/>
  <xsd:element id="sybx_LongTermIncentivePlan2015Member" name="LongTermIncentivePlan2015Member" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="sybx_ChangeInCarryingAmountOfOperatingLeaseRightOfUseAsset" name="ChangeInCarryingAmountOfOperatingLeaseRightOfUseAsset" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="sybx_ClassOfWarrantOrRightExercisePriceOfWarrantsPaidAtClosingOfOffering" name="ClassOfWarrantOrRightExercisePriceOfWarrantsPaidAtClosingOfOffering" type="dtr-types:perShareItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false"/>
  <xsd:element id="sybx_OptionsExercisableToPurchaseCommonStockMember" name="OptionsExercisableToPurchaseCommonStockMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="sybx_RelatedPartyTransactionCollaborationAgreementInitialTermExtended" name="RelatedPartyTransactionCollaborationAgreementInitialTermExtended" type="xbrli:durationItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false"/>
  <xsd:element id="sybx_ShareRepurchaseTextBlock" name="ShareRepurchaseTextBlock" type="dtr-types:textBlockItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false"/>
  <xsd:element id="sybx_JefferiesLLCMember" name="JefferiesLLCMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="sybx_AggregatePurchasePerShare" name="AggregatePurchasePerShare" type="dtr-types:perShareItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false"/>
  <xsd:element id="sybx_EstimatedProjectCostForAccessPersonalSupportAndOtherServices" name="EstimatedProjectCostForAccessPersonalSupportAndOtherServices" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="sybx_PrepaidResearchAndDevelopmentExpenses" name="PrepaidResearchAndDevelopmentExpenses" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="sybx_AzzurGroupLimitedLiabilityCompanyMember" name="AzzurGroupLimitedLiabilityCompanyMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="sybx_RepurchaseOfCommonStock" name="RepurchaseOfCommonStock" type="xbrli:sharesItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false"/>
  <xsd:element id="sybx_UnvestedRestrictedStockAwardsMember" name="UnvestedRestrictedStockAwardsMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="sybx_AvailableForSaleSecuritiesDisclosureTextBlock" name="AvailableForSaleSecuritiesDisclosureTextBlock" type="dtr-types:textBlockItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false"/>
  <xsd:element id="sybx_FairValueAssetMeasuredOnRecurringBasisLineItems" name="FairValueAssetMeasuredOnRecurringBasisLineItems" type="xbrli:stringItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="sybx_AggregatePurchase" name="AggregatePurchase" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="sybx_CurrentPrePaidResearchAndDevelopment" name="CurrentPrePaidResearchAndDevelopment" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="sybx_AccruedResearchAndDevelopmentCurrent" name="AccruedResearchAndDevelopmentCurrent" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="credit"/>
  <xsd:element id="sybx_AtTheMarketOfferingMember" name="AtTheMarketOfferingMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="sybx_AssetsAcquiredUnderOperatingLeaseObligation" name="AssetsAcquiredUnderOperatingLeaseObligation" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="sybx_TwoThousandSeventeenAndTwoThousandFifteenEquityIncentiveAwardPlanMember" name="TwoThousandSeventeenAndTwoThousandFifteenEquityIncentiveAwardPlanMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="sybx_AgreedToPayToRenovateAndUpgradeCleanroomSpace" name="AgreedToPayToRenovateAndUpgradeCleanroomSpace" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="sybx_PreFundedWarrantsMember" name="PreFundedWarrantsMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="sybx_IncreaseDecreaseInPrepaidResearchAndDevelopmentNetOfCurrentPortion" name="IncreaseDecreaseInPrepaidResearchAndDevelopmentNetOfCurrentPortion" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="sybx_WarrantsExercised" name="WarrantsExercised" type="xbrli:sharesItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false"/>
  <xsd:element id="sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOutstandingWeightedAverageExercisePriceAndAdditionalDisclosuresAbstract" name="ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOutstandingWeightedAverageExercisePriceAndAdditionalDisclosuresAbstract" type="xbrli:stringItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="sybx_NoncashInvestingItemsAbstract" name="NoncashInvestingItemsAbstract" type="xbrli:stringItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="sybx_ComputerAndOfficeEquipmentMember" name="ComputerAndOfficeEquipmentMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="sybx_ShareRepurchaseAbstract" name="ShareRepurchaseAbstract" type="xbrli:stringItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="sybx_USTreasuryAndGovernmentLongTermDebtSecuritiesMember" name="USTreasuryAndGovernmentLongTermDebtSecuritiesMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="sybx_NoncashPurchaseOfPropertyPlantAndEquipmentInAccountsPayableAndAccruedLiabilitiesAdjustments" name="NoncashPurchaseOfPropertyPlantAndEquipmentInAccountsPayableAndAccruedLiabilitiesAdjustments" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit"/>
  <xsd:element id="sybx_Scheduleoffairvalueassetsandliabilitiesmeasuredgrossunrealizedgainsandlossestabletextblock" name="Scheduleoffairvalueassetsandliabilitiesmeasuredgrossunrealizedgainsandlossestabletextblock" type="dtr-types:textBlockItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false"/>
  <xsd:element id="sybx_USGovernmentAgenciesDebtSecuritiesAndTreasuriesMember" name="USGovernmentAgenciesDebtSecuritiesAndTreasuriesMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="sybx_Cashequivalentsaccumulatedgrossunrealizedloss" name="Cashequivalentsaccumulatedgrossunrealizedloss" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="sybx_TreasuryStockShare" name="TreasuryStockShare" type="xbrli:sharesItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false"/>
  <xsd:element id="sybx_FairValueAssetMeasuredOnRecurringBasisTable" name="FairValueAssetMeasuredOnRecurringBasisTable" type="xbrli:stringItemType" substitutionGroup="xbrldt:hypercubeItem" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="sybx_OtherThanTemporaryImpairmentLossesInvestmentsNumberDebtSecuritiesAvailableForSale" name="OtherThanTemporaryImpairmentLossesInvestmentsNumberDebtSecuritiesAvailableForSale" type="xbrli:integerItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false"/>
  <xsd:element id="sybx_RocheCollaborationAndOptionAgreementMember" name="RocheCollaborationAndOptionAgreementMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="sybx_GinkgoBioworksIncMember" name="GinkgoBioworksIncMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
  <xsd:element id="sybx_Cashequivalentsaccumulatedgrossunrealizedgain" name="Cashequivalentsaccumulatedgrossunrealizedgain" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="credit"/>
  <xsd:element id="sybx_AmortizedCostFairValue" name="AmortizedCostFairValue" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="sybx_ProceedsFromEmployeeStockPurchasesAndExerciseOfStockOptions" name="ProceedsFromEmployeeStockPurchasesAndExerciseOfStockOptions" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="sybx_NonCurrentPrePaidResearchAndDevelopment" name="NonCurrentPrePaidResearchAndDevelopment" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="debit"/>
  <xsd:element id="sybx_IssuanceCostsIncludedInAccountsPayableAndAccruedExpenses" name="IssuanceCostsIncludedInAccountsPayableAndAccruedExpenses" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit"/>
  <xsd:element id="sybx_RelatedPartyTransactionCollaborationAgreementInitialTerm" name="RelatedPartyTransactionCollaborationAgreementInitialTerm" type="xbrli:durationItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false"/>
  <xsd:element id="sybx_NoncashFinancingItemsAbstract" name="NoncashFinancingItemsAbstract" type="xbrli:stringItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true"/>
</xsd:schema>
