diff --git a/clang/include/clang/Tooling/DependencyScanning/DependencyScanningFilesystem.h b/clang/include/clang/Tooling/DependencyScanning/DependencyScanningFilesystem.h
--- a/clang/include/clang/Tooling/DependencyScanning/DependencyScanningFilesystem.h
+++ b/clang/include/clang/Tooling/DependencyScanning/DependencyScanningFilesystem.h
@@ -153,8 +153,8 @@
   llvm::ErrorOr<std::unique_ptr<llvm::vfs::File>>
   openFileForRead(const Twine &Path) override;
 
-  /// The set of files that should not be minimized.
-  llvm::StringSet<> IgnoredFiles;
+  void clearIgnoredFiles() { IgnoredFiles.clear(); }
+  void ignoreFile(StringRef Filename);
 
 private:
   void setCachedEntry(StringRef Filename, const CachedFileSystemEntry *Entry) {
@@ -179,6 +179,8 @@
   /// excluded conditional directive skip mappings that are used by the
   /// currently active preprocessor.
   ExcludedPreprocessorDirectiveSkipMapping *PPSkipMappings;
+  /// The set of files that should not be minimized.
+  llvm::StringSet<> IgnoredFiles;
 };
 
 } // end namespace dependencies
diff --git a/clang/lib/Tooling/DependencyScanning/DependencyScanningFilesystem.cpp b/clang/lib/Tooling/DependencyScanning/DependencyScanningFilesystem.cpp
--- a/clang/lib/Tooling/DependencyScanning/DependencyScanningFilesystem.cpp
+++ b/clang/lib/Tooling/DependencyScanning/DependencyScanningFilesystem.cpp
@@ -149,9 +149,18 @@
   return shouldMinimize(Filename); // Only cache stat failures on source files.
 }
 
+void DependencyScanningWorkerFilesystem::ignoreFile(StringRef RawFilename) {
+  llvm::SmallString<256> Filename;
+  llvm::sys::path::native(RawFilename, Filename);
+  IgnoredFiles.insert(Filename);
+}
+
 llvm::ErrorOr<const CachedFileSystemEntry *>
 DependencyScanningWorkerFilesystem::getOrCreateFileSystemEntry(
-    const StringRef Filename) {
+    const StringRef RawFilename) {
+  llvm::SmallString<256> Filename;
+  llvm::sys::path::native(RawFilename, Filename);
+
   if (const CachedFileSystemEntry *Entry = getCachedEntry(Filename)) {
     return Entry;
   }
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
@@ -128,11 +128,11 @@
       // Add any filenames that were explicity passed in the build settings and
       // that might be opened, as we want to ensure we don't run source
       // minimization on them.
-      DepFS->IgnoredFiles.clear();
+      DepFS->clearIgnoredFiles();
       for (const auto &Entry : CI.getHeaderSearchOpts().UserEntries)
-        DepFS->IgnoredFiles.insert(Entry.Path);
+        DepFS->ignoreFile(Entry.Path);
       for (const auto &Entry : CI.getHeaderSearchOpts().VFSOverlayFiles)
-        DepFS->IgnoredFiles.insert(Entry);
+        DepFS->ignoreFile(Entry);
 
       // Support for virtual file system overlays on top of the caching
       // filesystem.