diff --git a/clang/lib/Tooling/DependencyScanning/ModuleDepCollector.cpp b/clang/lib/Tooling/DependencyScanning/ModuleDepCollector.cpp
--- a/clang/lib/Tooling/DependencyScanning/ModuleDepCollector.cpp
+++ b/clang/lib/Tooling/DependencyScanning/ModuleDepCollector.cpp
@@ -55,11 +55,6 @@
 
 void ModuleDepCollector::addOutputPaths(CompilerInvocation &CI,
                                         ModuleDeps &Deps) {
-  // These are technically *inputs* to the compilation, but we populate them
-  // here in order to make \c getModuleContextHash() independent of
-  // \c lookupModuleOutput().
-  addModuleFiles(CI, Deps.ClangModuleDeps);
-
   CI.getFrontendOpts().OutputFile =
       Consumer.lookupModuleOutput(Deps.ID, ModuleOutputKind::ModuleFile);
   if (!CI.getDiagnosticOpts().DiagnosticSerializationFile.empty())
@@ -156,6 +151,9 @@
   for (const auto &PrebuiltModule : Deps.PrebuiltModuleDeps)
     CI.getFrontendOpts().ModuleFiles.push_back(PrebuiltModule.PCMFile);
 
+  // Add module file inputs from dependencies.
+  addModuleFiles(CI, Deps.ClangModuleDeps);
+
   // Remove any macro definitions that are explicitly ignored.
   if (!CI.getHeaderSearchOpts().ModulesIgnoreMacros.empty()) {
     llvm::erase_if(