diff --git a/clang/lib/Tooling/DependencyScanning/DependencyScanningWorker.cpp b/clang/lib/Tooling/DependencyScanning/DependencyScanningWorker.cpp
--- a/clang/lib/Tooling/DependencyScanning/DependencyScanningWorker.cpp
+++ b/clang/lib/Tooling/DependencyScanning/DependencyScanningWorker.cpp
@@ -192,6 +192,11 @@
     ScanInstance.getFrontendOpts().ModulesShareFileManager = false;
 
     ScanInstance.setFileManager(FileMgr);
+    // Support for virtual file system overlays.
+    FileMgr->setVirtualFileSystem(createVFSFromCompilerInvocation(
+        ScanInstance.getInvocation(), ScanInstance.getDiagnostics(),
+        FileMgr->getVirtualFileSystemPtr()));
+
     ScanInstance.createSourceManager(*FileMgr);
 
     llvm::StringSet<> PrebuiltModulesInputFiles;
@@ -206,12 +211,6 @@
 
     // Use the dependency scanning optimized file system if requested to do so.
     if (DepFS) {
-      // Support for virtual file system overlays on top of the caching
-      // filesystem.
-      FileMgr->setVirtualFileSystem(createVFSFromCompilerInvocation(
-          ScanInstance.getInvocation(), ScanInstance.getDiagnostics(),
-          FileMgr->getVirtualFileSystemPtr()));
-
       llvm::IntrusiveRefCntPtr<DependencyScanningWorkerFilesystem> LocalDepFS =
           DepFS;
       ScanInstance.getPreprocessorOpts().DependencyDirectivesForFile =
diff --git a/clang/test/ClangScanDeps/vfsoverlay.cpp b/clang/test/ClangScanDeps/vfsoverlay.cpp
--- a/clang/test/ClangScanDeps/vfsoverlay.cpp
+++ b/clang/test/ClangScanDeps/vfsoverlay.cpp
@@ -8,8 +8,8 @@
 // RUN: cp %S/Inputs/header.h %t.dir/Inputs/header.h
 // RUN: sed -e "s|DIR|%/t.dir|g" %S/Inputs/vfsoverlay_cdb.json > %t.cdb
 //
-// RUN: clang-scan-deps -compilation-database %t.cdb -j 1 | \
-// RUN:   FileCheck %s
+// RUN: clang-scan-deps -compilation-database %t.cdb -mode preprocess-dependency-directives -j 1 | FileCheck %s
+// RUN: clang-scan-deps -compilation-database %t.cdb -mode preprocess                       -j 1 | FileCheck %s
 
 #include "not_real.h"