diff --git a/clang/lib/Tooling/DependencyScanning/DependencyScanningTool.cpp b/clang/lib/Tooling/DependencyScanning/DependencyScanningTool.cpp
--- a/clang/lib/Tooling/DependencyScanning/DependencyScanningTool.cpp
+++ b/clang/lib/Tooling/DependencyScanning/DependencyScanningTool.cpp
@@ -32,14 +32,17 @@
   for (const PrebuiltModuleDep &PMD : PrebuiltModuleDeps)
     Args.push_back("-fmodule-file=" + PMD.PCMFile);
 
-  // This argument is unused in explicit compiles.
-  llvm::erase_if(Args, [](const std::string &Arg) {
-    return Arg.find("-fmodules-cache-path=") == 0;
+  // These arguments are unused in explicit compiles.
+  llvm::erase_if(Args, [](StringRef Arg) {
+    if (Arg.consume_front("-fmodules-")) {
+      return Arg.startswith("cache-path=") ||
+             Arg.startswith("prune-interval=") ||
+             Arg.startswith("prune-after=") ||
+             Arg == "validate-once-per-build-session";
+    }
+    return Arg.startswith("-fbuild-session-file=");
   });
 
-  // TODO: Filter out the remaining implicit modules leftovers
-  // (e.g. "-fmodules-prune-interval=" or "-fmodules-prune-after=").
-
   return Args;
 }
 
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
@@ -61,9 +61,17 @@
   CI.getLangOpts()->ModuleName = Deps.ID.ModuleName;
   CI.getFrontendOpts().IsSystemModule = Deps.IsSystem;
 
+  // Disable implicit modules and canonicalize options that are only used by
+  // implicit modules.
   CI.getLangOpts()->ImplicitModules = false;
   CI.getHeaderSearchOpts().ImplicitModuleMaps = false;
   CI.getHeaderSearchOpts().ModuleCachePath.clear();
+  CI.getHeaderSearchOpts().ModulesValidateOncePerBuildSession = false;
+  CI.getHeaderSearchOpts().BuildSessionTimestamp = 0;
+  // The specific values we canonicalize to for pruning don't affect behaviour,
+  /// so use the default values so they will be dropped from the command-line.
+  CI.getHeaderSearchOpts().ModuleCachePruneInterval = 7 * 24 * 60 * 60;
+  CI.getHeaderSearchOpts().ModuleCachePruneAfter = 31 * 24 * 60 * 60;
 
   // Report the prebuilt modules this module uses.
   for (const auto &PrebuiltModule : Deps.PrebuiltModuleDeps)
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-cache-path=DIR/cache -include DIR/header.h -grecord-command-line -o DIR/tu.o",
+    "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",
     "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
@@ -2,10 +2,13 @@
 // compatible with the semantics of modules or are likely to differ between
 // identical modules discovered from different translation units. This test
 // checks such arguments are removed from the command-lines: '-include',
-// '-dwarf-debug-flag' and '-main-file-name'.
+// '-dwarf-debug-flag' and '-main-file-name'. Similarly, several arguments
+// such as '-fmodules-cache-path=' are only relevant for implicit modules, and
+// are removed to better-canonicalize the compilation.
 
 // RUN: rm -rf %t && mkdir %t
 // RUN: cp %S/Inputs/removed-args/* %t
+// RUN: touch %t/build-session
 
 // RUN: sed "s|DIR|%/t|g" %S/Inputs/removed-args/cdb.json.template > %t/cdb.json
 // RUN: clang-scan-deps -compilation-database %t/cdb.json -format experimental-full > %t/result.json
@@ -21,6 +24,11 @@
 // CHECK-NOT:          "-dwarf-debug-flags"
 // CHECK-NOT:          "-main-file-name"
 // CHECK-NOT:          "-include"
+// CHECK-NOT:          "-fmodules-cache-path=
+// CHECK-NOT:          "-fmodules-validate-once-per-build-session"
+// CHECK-NOT:          "-fbuild-session-timestamp=
+// CHECK-NOT:          "-fmodules-prune-interval=
+// CHECK-NOT:          "-fmodules-prune-after=
 // CHECK:            ],
 // CHECK-NEXT:       "context-hash": "[[HASH_MOD_HEADER:.*]]",
 // CHECK-NEXT:       "file-deps": [
@@ -34,7 +42,14 @@
 // CHECK-NEXT:       "clang-modulemap-file": "[[PREFIX]]/module.modulemap",
 // CHECK-NEXT:       "command-line": [
 // CHECK-NEXT:         "-cc1"
+// CHECK-NOT:          "-dwarf-debug-flags"
+// CHECK-NOT:          "-main-file-name"
 // CHECK-NOT:          "-include"
+// CHECK-NOT:          "-fmodules-cache-path=
+// CHECK-NOT:          "-fmodules-validate-once-per-build-session"
+// CHECK-NOT:          "-fbuild-session-timestamp=
+// CHECK-NOT:          "-fmodules-prune-interval=
+// CHECK-NOT:          "-fmodules-prune-after=
 // CHECK:            ],
 // CHECK-NEXT:       "context-hash": "[[HASH_MOD_TU:.*]]",
 // CHECK-NEXT:       "file-deps": [
@@ -57,6 +72,14 @@
 // CHECK-NEXT:           "module-name": "ModTU"
 // CHECK-NEXT:         }
 // CHECK-NEXT:       ]
+// CHECK-NEXT:       "command-line": [
+// CHECK-NEXT:         "-fsyntax-only",
+// CHECK-NOT:          "-fmodules-cache-path=
+// CHECK-NOT:          "-fmodules-validate-once-per-build-session"
+// CHECK-NOT:          "-fbuild-session-file=
+// CHECK-NOT:          "-fmodules-prune-interval=
+// CHECK-NOT:          "-fmodules-prune-after=
+// CHECK:            ],
 // CHECK:          }
 // CHECK-NEXT:   ]
 // CHECK-NEXT: }