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
@@ -97,8 +97,15 @@
   // units.
   CI.getFrontendOpts().Inputs.clear();
   CI.getFrontendOpts().OutputFile.clear();
+
+  // TODO: Figure out better way to set options to their default value.
   CI.getCodeGenOpts().MainFileName.clear();
   CI.getCodeGenOpts().DwarfDebugFlags.clear();
+  if (!CI.getLangOpts()->ModulesCodegen) {
+    CI.getCodeGenOpts().DebugCompilationDir.clear();
+    CI.getCodeGenOpts().CoverageCompilationDir.clear();
+  }
+
   // Map output paths that affect behaviour to "-" so their existence is in the
   // context hash. The final path will be computed in addOutputPaths.
   if (!CI.getDiagnosticOpts().DiagnosticSerializationFile.empty())
diff --git a/clang/test/ClangScanDeps/Inputs/removed-args/cdb.json.template b/clang/test/ClangScanDeps/Inputs/removed-args/cdb.json.template
--- a/clang/test/ClangScanDeps/Inputs/removed-args/cdb.json.template
+++ b/clang/test/ClangScanDeps/Inputs/removed-args/cdb.json.template
@@ -1,7 +1,7 @@
 [
   {
     "directory": "DIR",
-    "command": "clang -fsyntax-only DIR/tu.c -fmodules -fimplicit-module-maps -fmodules-validate-once-per-build-session -fbuild-session-file=DIR/build-session -fmodules-prune-interval=123 -fmodules-prune-after=123 -fmodules-cache-path=DIR/cache -include DIR/header.h -grecord-command-line -o DIR/tu.o -serialize-diagnostics DIR/tu.diag -MT tu -MD -MF DIR/tu.d",
+    "command": "clang -fsyntax-only DIR/tu.c -fmodules -fimplicit-module-maps -fmodules-validate-once-per-build-session -fbuild-session-file=DIR/build-session -fmodules-prune-interval=123 -fmodules-prune-after=123 -fmodules-cache-path=DIR/cache -include DIR/header.h -grecord-command-line -fdebug-compilation-dir=DIR/debug -fcoverage-compilation-dir=DIR/coverage -o DIR/tu.o -serialize-diagnostics DIR/tu.diag -MT tu -MD -MF DIR/tu.d",
     "file": "DIR/tu.c"
   }
 ]
diff --git a/clang/test/ClangScanDeps/removed-args.c b/clang/test/ClangScanDeps/removed-args.c
--- a/clang/test/ClangScanDeps/removed-args.c
+++ b/clang/test/ClangScanDeps/removed-args.c
@@ -21,6 +21,8 @@
 // CHECK-NEXT:       "clang-modulemap-file": "[[PREFIX]]/module.modulemap",
 // CHECK-NEXT:       "command-line": [
 // CHECK-NEXT:         "-cc1"
+// CHECK-NOT:          "-fdebug-compilation-dir="
+// CHECK-NOT:          "-fcoverage-compilation-dir="
 // CHECK-NOT:          "-dwarf-debug-flags"
 // CHECK-NOT:          "-main-file-name"
 // CHECK-NOT:          "-include"
@@ -42,6 +44,8 @@
 // CHECK-NEXT:       "clang-modulemap-file": "[[PREFIX]]/module.modulemap",
 // CHECK-NEXT:       "command-line": [
 // CHECK-NEXT:         "-cc1"
+// CHECK-NOT:          "-fdebug-compilation-dir=
+// CHECK-NOT:          "-fcoverage-compilation-dir=
 // CHECK-NOT:          "-dwarf-debug-flags"
 // CHECK-NOT:          "-main-file-name"
 // CHECK-NOT:          "-include"