diff --git a/Sources/XcodeProj/Utils/ReferenceGenerator.swift b/Sources/XcodeProj/Utils/ReferenceGenerator.swift
index 221352355..5d2617af4 100644
--- a/Sources/XcodeProj/Utils/ReferenceGenerator.swift
+++ b/Sources/XcodeProj/Utils/ReferenceGenerator.swift
@@ -18,6 +18,11 @@ final class ReferenceGenerator: ReferenceGenerating {
     var references: Set<String> = []
     /// The type name and reference acronym of each object type, which only depend on the type.
     private var typeNamesAndAcronyms: [ObjectIdentifier: (typeName: String, acronym: String)] = [:]
+    /// Build phase membership exception sets waiting for their build phases' references, with their identifiers.
+    private var buildPhaseMembershipExceptionSets: [(
+        exceptionSet: PBXFileSystemSynchronizedGroupBuildPhaseMembershipExceptionSet,
+        identifiers: [String]
+    )] = []
 
     init(outputSettings: PBXOutputSettings) {
         self.outputSettings = outputSettings
@@ -65,6 +70,17 @@ final class ReferenceGenerator: ReferenceGenerating {
         let targets: [PBXTarget] = project.targets
         try targets.forEach { try generateTargetReferences($0, identifiers: identifiers) }
 
+        // Build phase membership exception sets, whose references derive from their build phases' references, which
+        // the targets have just generated.
+        for (exceptionSet, identifiers) in buildPhaseMembershipExceptionSets {
+            var identifiers = identifiers
+            if let buildPhase = exceptionSet.buildPhase {
+                identifiers.append(buildPhase.reference.value)
+            }
+            fixReference(for: exceptionSet, identifiers: identifiers)
+        }
+        buildPhaseMembershipExceptionSets = []
+
         /// Configuration list
         if let configurationList: XCConfigurationList = project.buildConfigurationListReference.getObject() {
             try generateConfigurationListReferences(configurationList, identifiers: identifiers)
@@ -202,10 +218,8 @@ final class ReferenceGenerator: ReferenceGenerating {
             }
             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)
+            // Its build phase may not have a permanent reference yet, so it's generated after the targets.
+            buildPhaseMembershipExceptionSets.append((buildPhaseException, identifiers))
         }
     }
 
diff --git a/Tests/XcodeProjTests/Utils/ReferenceFixingTests.swift b/Tests/XcodeProjTests/Utils/ReferenceFixingTests.swift
index 1d365c82f..6e6f57397 100644
--- a/Tests/XcodeProjTests/Utils/ReferenceFixingTests.swift
+++ b/Tests/XcodeProjTests/Utils/ReferenceFixingTests.swift
@@ -33,7 +33,8 @@ struct ReferenceFixingTests {
     }
 
     #if os(macOS) || (os(Linux) && compiler(>=6.1))
-        /// Writing a project whose references are all temporary moves every object it decodes to a permanent reference.
+        /// Writing a project whose references are all temporary moves every object it decodes to a permanent reference,
+        /// and gives each the same reference every time.
         @Test(arguments: [
             "iOS/Project.xcodeproj",
             "iOS/AppWithExtensions/AppWithExtensions.xcodeproj",
@@ -43,15 +44,19 @@ struct ReferenceFixingTests {
             "Xcode16ProjectReferenceOrder/Test.xcodeproj",
         ])
         func writingAProjectWithTemporaryReferences_keepsEveryObject(fixture: String) throws {
-            let pbxproj = try PBXProj(path: fixturesPath() + fixture + "project.pbxproj")
-            let objects = objectCountsByType(pbxproj.objects)
-            pbxproj.objects.invalidateReferences()
-
-            let data = try #require(try pbxproj.dataRepresentation())
+            func write() throws -> (objects: [String: Int], data: Data) {
+                let pbxproj = try PBXProj(path: fixturesPath() + fixture + "project.pbxproj")
+                let objects = objectCountsByType(pbxproj.objects)
+                pbxproj.objects.invalidateReferences()
+                return try (objects, #require(try pbxproj.dataRepresentation()))
+            }
+
+            let (objects, data) = try write()
             let written = try PBXProj(data: data)
 
             #expect(objectCountsByType(written.objects) == objects)
             #expect(!String(decoding: data, as: UTF8.self).contains("TEMP_"))
+            #expect(try write().data == data)
         }
     #endif
 
diff --git a/Tests/XcodeProjTests/Utils/ReferenceGeneratorTests.swift b/Tests/XcodeProjTests/Utils/ReferenceGeneratorTests.swift
index a09c79cb1..c1621addb 100644
--- a/Tests/XcodeProjTests/Utils/ReferenceGeneratorTests.swift
+++ b/Tests/XcodeProjTests/Utils/ReferenceGeneratorTests.swift
@@ -155,6 +155,41 @@ class ReferenceGeneratorTests: XCTestCase {
         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")
     }
+
+    func test_projectWithFilesystemSynchronizedRootGroupWithBuildPhaseException_generatesDeterministicIdentifiers() throws {
+        // The build phase starts with a temporary reference, as it does in a project created in code.
+        func generateProject() throws -> [String] {
+            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)
+
+            return [buildPhase, buildPhaseException, syncedGroup].map(\.reference.value)
+        }
+
+        let firstReferences = try generateProject()
+        let secondReferences = try generateProject()
+
+        XCTAssertEqual(firstReferences, secondReferences)
+    }
 }
 
 private extension PBXProj {