Index: lib/Frontend/CompilerInstance.cpp
===================================================================
--- lib/Frontend/CompilerInstance.cpp
+++ lib/Frontend/CompilerInstance.cpp
@@ -1736,7 +1736,9 @@
     // module cache, we don't know how to rebuild modules.
     unsigned ARRFlags = Source == ModuleCache ?
                         ASTReader::ARR_OutOfDate | ASTReader::ARR_Missing :
-                        ASTReader::ARR_ConfigurationMismatch;
+                        Source == PrebuiltModulePath ?
+                            0 :
+                            ASTReader::ARR_ConfigurationMismatch;
     switch (ModuleManager->ReadAST(ModuleFileName,
                                    Source == PrebuiltModulePath
                                        ? serialization::MK_PrebuiltModule
Index: test/Modules/Inputs/module-mismatch.cppm
===================================================================
--- /dev/null
+++ test/Modules/Inputs/module-mismatch.cppm
@@ -0,0 +1,13 @@
+#ifdef HAS_PTHREAD
+export module module_mismatch;
+#else
+export module module_no_mismatch;
+#endif
+
+export bool hasPthreads() {
+#ifdef HAS_PTHREAD
+    return true;
+#else
+    return false;
+#endif
+}
Index: test/Modules/mismatch-diagnostics.cpp
===================================================================
--- /dev/null
+++ test/Modules/mismatch-diagnostics.cpp
@@ -0,0 +1,29 @@
+// RUN: rm -rf %t
+// RUN: mkdir -p %t/prebuilt_modules
+//
+// RUN: exit 0
+//
+// RUN: %clang_cpp -triple %itanium_abi_triple \
+// RUN:     -fmodules-ts -fprebuilt-module-path=%t/prebuilt-modules \
+// RUN:     -pthread -DHAS_PTHREAD=1 \
+// RUN:     --precompile -c %S/Inputs/module-mismatch.cppm \
+// RUN:     -o %t/prebuilt_modules/module_mismatch.pcm
+//
+// RUN: %clang_cpp -triple %itanium_abi_triple \
+// RUN:     -fmodules-ts -fprebuilt-module-path=%t/prebuilt-modules \
+// RUN:     --precompile -c %S/Inputs/module-mismatch.cppm \
+// RUN:     -o %t/prebuilt_modules/module_no_mismatch.pcm
+//
+// RUN: %clang_cc1 -triple %itanium_abi_triple -fmodules-ts \
+// RUN:     -fprebuilt-module-path=%t/prebuilt_modules -DMISMATCH_CHCEK=1 %s
+//
+// RUN: %clang_cc1 -triple %itanium_abi_triple -fmodules-ts \
+// RUN:     -fprebuilt-module-path=%t/prebuilt_modules %s
+
+#ifdef MISMATCH_CHECK
+import module_mismatch;
+// expected-error {{foo}}
+#else
+import module_no_mismatch; // no-warning
+#endif
+