diff --git a/Sources/XcodeProj/Utils/ReferenceGenerator.swift b/Sources/XcodeProj/Utils/ReferenceGenerator.swift
index 01f0267e9..21df39128 100644
--- a/Sources/XcodeProj/Utils/ReferenceGenerator.swift
+++ b/Sources/XcodeProj/Utils/ReferenceGenerator.swift
@@ -176,6 +176,35 @@ final class ReferenceGenerator: ReferenceGenerating {
         }
 
         fixReference(for: synchronizedRootGroup, identifiers: identifiers)
+        
+        // Generate references for exception sets
+        if let exceptions = synchronizedRootGroup.exceptions {
+            try exceptions.forEach { exception in
+                try generateExceptionSetReferences(exception, identifiers: identifiers)
+            }
+        }
+    }
+    
+    /// Generates the reference for an exception set object.
+    ///
+    /// - Parameters:
+    ///   - exceptionSet: exception set instance.
+    ///   - identifiers: list of identifiers.
+    private func generateExceptionSetReferences(_ exceptionSet: PBXFileSystemSynchronizedExceptionSet,
+                                                identifiers: [String]) throws {
+        var identifiers = identifiers
+        
+        if let buildFileException = exceptionSet as? PBXFileSystemSynchronizedBuildFileExceptionSet {
+            if let target = buildFileException.target {
+                identifiers.append(target.reference.value)
+            }
+            fixReference(for: buildFileException, identifiers: identifiers)
+        } else if let buildPhaseException = exceptionSet as? PBXFileSystemSynchronizedGroupBuildPhaseMembershipExceptionSet {
+            if let buildPhase = buildPhaseException.buildPhase {
+                identifiers.append(buildPhase.reference.value)
+            }
+            fixReference(for: buildPhaseException, identifiers: identifiers)
+        }
     }
 
     /// Generates the reference for a configuration list object.
diff --git a/Tests/XcodeProjTests/Utils/ReferenceGeneratorTests.swift b/Tests/XcodeProjTests/Utils/ReferenceGeneratorTests.swift
index af3a2f1b1..de9efd080 100644
--- a/Tests/XcodeProjTests/Utils/ReferenceGeneratorTests.swift
+++ b/Tests/XcodeProjTests/Utils/ReferenceGeneratorTests.swift
@@ -98,6 +98,63 @@ class ReferenceGeneratorTests: XCTestCase {
 
         XCTAssert(!syncedGroup.reference.temporary)
     }
+    
+    func test_projectWithFilesystemSynchronizedRootGroupWithExceptions_convertsReferencesToPermanent() throws {
+        let project = PBXProj(rootObject: nil, objectVersion: 0, archiveVersion: 0, classes: [:], objects: [])
+        let pbxProject = project.makeProject()
+
+        let target = project.makeTarget()
+        pbxProject.targets.append(target)
+        
+        let buildFileException = PBXFileSystemSynchronizedBuildFileExceptionSet(
+            target: target,
+            membershipExceptions: ["Info.plist"],
+            publicHeaders: nil,
+            privateHeaders: nil,
+            additionalCompilerFlagsByRelativePath: nil,
+            attributesByRelativePath: nil
+        )
+        project.add(object: buildFileException)
+        
+        let syncedGroup = project.makeSynchronizedRootGroup(exceptions: [buildFileException])
+        target.fileSystemSynchronizedGroups = [syncedGroup]
+
+        let referenceGenerator = ReferenceGenerator(outputSettings: PBXOutputSettings())
+        try referenceGenerator.generateReferences(proj: project)
+
+        XCTAssert(!syncedGroup.reference.temporary, "Synced group reference should not be temporary")
+        XCTAssert(!buildFileException.reference.temporary, "Build file exception reference should not be temporary")
+        XCTAssertFalse(buildFileException.reference.value.hasPrefix("TEMP_"), "Build file exception reference should not have TEMP_ prefix")
+    }
+    
+    func test_projectWithFilesystemSynchronizedRootGroupWithBuildPhaseException_convertsReferencesToPermanent() throws {
+        let project = PBXProj(rootObject: nil, objectVersion: 0, archiveVersion: 0, classes: [:], objects: [])
+        let pbxProject = project.makeProject()
+
+        let target = project.makeTarget()
+        pbxProject.targets.append(target)
+        
+        let buildPhase = PBXSourcesBuildPhase()
+        project.add(object: buildPhase)
+        target.buildPhases.append(buildPhase)
+        
+        let buildPhaseException = PBXFileSystemSynchronizedGroupBuildPhaseMembershipExceptionSet(
+            buildPhase: buildPhase,
+            membershipExceptions: ["ExcludedFile.swift"],
+            attributesByRelativePath: nil
+        )
+        project.add(object: buildPhaseException)
+        
+        let syncedGroup = project.makeSynchronizedRootGroup(exceptions: [buildPhaseException])
+        target.fileSystemSynchronizedGroups = [syncedGroup]
+
+        let referenceGenerator = ReferenceGenerator(outputSettings: PBXOutputSettings())
+        try referenceGenerator.generateReferences(proj: project)
+
+        XCTAssert(!syncedGroup.reference.temporary, "Synced group reference should not be temporary")
+        XCTAssert(!buildPhaseException.reference.temporary, "Build phase exception reference should not be temporary")
+        XCTAssertFalse(buildPhaseException.reference.value.hasPrefix("TEMP_"), "Build phase exception reference should not have TEMP_ prefix")
+    }
 }
 
 private extension PBXProj {
@@ -192,11 +249,12 @@ private extension PBXProj {
         return target
     }
 
-    func makeSynchronizedRootGroup() -> PBXFileSystemSynchronizedRootGroup {
+    func makeSynchronizedRootGroup(exceptions: [PBXFileSystemSynchronizedExceptionSet] = []) -> PBXFileSystemSynchronizedRootGroup {
         let syncedGroup = PBXFileSystemSynchronizedRootGroup(
             sourceTree: .group,
             path: "SyncedPath",
-            name: "SyncedGroup"
+            name: "SyncedGroup",
+            exceptions: exceptions
         )
         add(object: syncedGroup)
         rootObject!.mainGroup.children.append(syncedGroup)