diff --git a/clang/lib/Tooling/DependencyScanning/DependencyScanningWorker.cpp b/clang/lib/Tooling/DependencyScanning/DependencyScanningWorker.cpp
index 2b882f8a5e079..76f3d950a13b8 100644
--- a/clang/lib/Tooling/DependencyScanning/DependencyScanningWorker.cpp
+++ b/clang/lib/Tooling/DependencyScanning/DependencyScanningWorker.cpp
@@ -296,7 +296,7 @@ class DependencyScanningAction : public tooling::ToolAction {
         DisableFree(DisableFree), ModuleName(ModuleName) {}
 
   bool runInvocation(std::shared_ptr<CompilerInvocation> Invocation,
-                     FileManager *FileMgr,
+                     FileManager *DriverFileMgr,
                      std::shared_ptr<PCHContainerOperations> PCHContainerOps,
                      DiagnosticConsumer *DiagConsumer) override {
     // Make a deep copy of the original Clang invocation.
@@ -342,12 +342,13 @@ class DependencyScanningAction : public tooling::ToolAction {
     ScanInstance.getHeaderSearchOpts().ModulesIncludeVFSUsage =
         any(OptimizeArgs & ScanningOptimizations::VFS);
 
-    ScanInstance.setFileManager(FileMgr);
     // Support for virtual file system overlays.
-    FileMgr->setVirtualFileSystem(createVFSFromCompilerInvocation(
+    auto FS = createVFSFromCompilerInvocation(
         ScanInstance.getInvocation(), ScanInstance.getDiagnostics(),
-        FileMgr->getVirtualFileSystemPtr()));
+        DriverFileMgr->getVirtualFileSystemPtr());
 
+    // Create a new FileManager to match the invocation's FileSystemOptions.
+    auto *FileMgr = ScanInstance.createFileManager(FS);
     ScanInstance.createSourceManager(*FileMgr);
 
     // Store the list of prebuilt module files into header search options. This
@@ -624,9 +625,8 @@ bool DependencyScanningWorker::computeDependencies(
       ModifiedCommandLine ? *ModifiedCommandLine : CommandLine;
   auto &FinalFS = ModifiedFS ? ModifiedFS : BaseFS;
 
-  FileSystemOptions FSOpts;
-  FSOpts.WorkingDir = WorkingDirectory.str();
-  auto FileMgr = llvm::makeIntrusiveRefCnt<FileManager>(FSOpts, FinalFS);
+  auto FileMgr =
+      llvm::makeIntrusiveRefCnt<FileManager>(FileSystemOptions{}, FinalFS);
 
   std::vector<const char *> FinalCCommandLine(FinalCommandLine.size(), nullptr);
   llvm::transform(FinalCommandLine, FinalCCommandLine.begin(),
diff --git a/clang/test/ClangScanDeps/working-directory-option.c b/clang/test/ClangScanDeps/working-directory-option.c
new file mode 100644
index 0000000000000..d57497d405d30
--- /dev/null
+++ b/clang/test/ClangScanDeps/working-directory-option.c
@@ -0,0 +1,30 @@
+// Test that -working-directory works even when it differs from the working
+// directory of the filesystem.
+
+// RUN: rm -rf %t
+// RUN: mkdir -p %t/other
+// RUN: split-file %s %t
+// RUN: sed -e "s|DIR|%/t|g" %t/cdb.json.template > %t/cdb.json
+
+// RUN: clang-scan-deps -compilation-database %t/cdb.json -format experimental-full \
+// RUN:   > %t/deps.json
+
+// RUN: cat %t/deps.json | sed 's:\\\\\?:/:g' | FileCheck %s -DPREFIX=%/t
+
+// CHECK:      "file-deps": [
+// CHECK-NEXT:   "[[PREFIX]]/cwd/t.c"
+// CHECK-NEXT:   "[[PREFIX]]/cwd/relative/h1.h"
+// CHECK-NEXT: ]
+// CHECK-NEXT: "input-file": "[[PREFIX]]/cwd/t.c"
+
+//--- cdb.json.template
+[{
+  "directory": "DIR/other",
+  "command": "clang -c t.c -I relative -working-directory DIR/cwd",
+  "file": "DIR/cwd/t.c"
+}]
+
+//--- cwd/relative/h1.h
+
+//--- cwd/t.c
+#include "h1.h"