diff --git a/clang/include/clang/Lex/Preprocessor.h b/clang/include/clang/Lex/Preprocessor.h
--- a/clang/include/clang/Lex/Preprocessor.h
+++ b/clang/include/clang/Lex/Preprocessor.h
@@ -1335,6 +1335,16 @@
 
   /// \}
 
+  /// Mark the given module as affecting the current module or translation unit.
+  void markModuleAsAffecting(Module *M) {
+    if (!BuildingSubmoduleStack.empty()) {
+      if (M != BuildingSubmoduleStack.back().M)
+        BuildingSubmoduleStack.back().M->AffectingModules.insert(M);
+    } else {
+      AffectingModules.insert(M);
+    }
+  }
+
   /// Get the set of top-level modules that affected preprocessing, but were not
   /// imported.
   const llvm::SmallSetVector<Module *, 2> &getAffectingModules() const {
diff --git a/clang/lib/Frontend/CompilerInstance.cpp b/clang/lib/Frontend/CompilerInstance.cpp
--- a/clang/lib/Frontend/CompilerInstance.cpp
+++ b/clang/lib/Frontend/CompilerInstance.cpp
@@ -2013,8 +2013,7 @@
     // match Foo_Private and emit a warning asking for the user to write
     // @import Foo_Private instead. FIXME: remove this when existing clients
     // migrate off of Foo.Private syntax.
-    if (!Sub && PP->getLangOpts().ImplicitModules && Name == "Private" &&
-        Module == Module->getTopLevelModule()) {
+    if (!Sub && Name == "Private" && Module == Module->getTopLevelModule()) {
       SmallString<128> PrivateModule(Module->Name);
       PrivateModule.append("_Private");
 
@@ -2028,6 +2027,7 @@
         Sub = loadModule(ImportLoc, PrivPath, Visibility, IsInclusionDirective);
       if (Sub) {
         MapPrivateSubModToTopLevel = true;
+        PP->markModuleAsAffecting(Module);
         if (!getDiagnostics().isIgnored(
                 diag::warn_no_priv_submodule_use_toplevel, ImportLoc)) {
           getDiagnostics().Report(Path[I].second,
diff --git a/clang/lib/Lex/PPDirectives.cpp b/clang/lib/Lex/PPDirectives.cpp
--- a/clang/lib/Lex/PPDirectives.cpp
+++ b/clang/lib/Lex/PPDirectives.cpp
@@ -2281,13 +2281,8 @@
     if (Imported) {
       Action = Import;
     } else if (Imported.isMissingExpected()) {
-      Module *M = static_cast<Module *>(Imported)->getTopLevelModule();
-      if (!BuildingSubmoduleStack.empty()) {
-        if (Imported != BuildingSubmoduleStack.back().M)
-          BuildingSubmoduleStack.back().M->AffectingModules.insert(M);
-      } else {
-        AffectingModules.insert(M);
-      }
+      markModuleAsAffecting(
+          static_cast<Module *>(Imported)->getTopLevelModule());
       // We failed to find a submodule that we assumed would exist (because it
       // was in the directory of an umbrella header, for instance), but no
       // actual module containing it exists (because the umbrella header is
diff --git a/clang/test/ClangScanDeps/modules-implicit-dot-private.m b/clang/test/ClangScanDeps/modules-implicit-dot-private.m
new file mode 100644
--- /dev/null
+++ b/clang/test/ClangScanDeps/modules-implicit-dot-private.m
@@ -0,0 +1,85 @@
+// This test checks that modules loaded during compilation (but not imported)
+// are still reported as dependencies.
+
+// RUN: rm -rf %t && mkdir %t
+// RUN: split-file %s %t
+
+//--- frameworks/FW.framework/Modules/module.modulemap
+framework module FW { umbrella header "FW.h" }
+//--- frameworks/FW.framework/Headers/FW.h
+//--- frameworks/FW.framework/Modules/module.private.modulemap
+framework module FW_Private { umbrella header "FW_Private.h" }
+//--- frameworks/FW.framework/PrivateHeaders/FW_Private.h
+
+//--- cdb.json.template
+[{
+  "file": "DIR/tu.m",
+  "directory": "DIR",
+  "command": "clang -fmodules -fmodules-cache-path=DIR/cache -iframework DIR/frameworks -c DIR/tu.m -o DIR/tu.o"
+}]
+//--- tu.m
+@import FW.Private;
+
+// 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 > %t/result.json
+// RUN: cat %t/result.json | sed 's:\\\\\?:/:g' | FileCheck %s -DPREFIX=%/t
+// CHECK:      {
+// CHECK-NEXT:   "modules": [
+// CHECK-NEXT:     {
+// CHECK-NEXT:       "clang-module-deps": [],
+// CHECK-NEXT:       "clang-modulemap-file": "[[PREFIX]]/frameworks/FW.framework/Modules/module.modulemap",
+// CHECK-NEXT:       "command-line": [
+// CHECK:            ],
+// CHECK-NEXT:       "context-hash": "{{.*}}",
+// CHECK-NEXT:       "file-deps": [
+// CHECK-NEXT:         "[[PREFIX]]/frameworks/FW.framework/Headers/FW.h",
+// CHECK-NEXT:         "[[PREFIX]]/frameworks/FW.framework/Modules/module.modulemap",
+// CHECK-NEXT:         "[[PREFIX]]/frameworks/FW.framework/Modules/module.private.modulemap"
+// CHECK-NEXT:       ],
+// CHECK-NEXT:       "name": "FW"
+// CHECK-NEXT:     },
+// CHECK-NEXT:     {
+// CHECK-NEXT:       "clang-module-deps": [],
+// CHECK-NEXT:       "clang-modulemap-file": "[[PREFIX]]/frameworks/FW.framework/Modules/module.private.modulemap",
+// CHECK-NEXT:       "command-line": [
+// CHECK:            ],
+// CHECK-NEXT:       "context-hash": "{{.*}}",
+// CHECK-NEXT:       "file-deps": [
+// CHECK-NEXT:         "[[PREFIX]]/frameworks/FW.framework/Modules/module.modulemap",
+// CHECK-NEXT:         "[[PREFIX]]/frameworks/FW.framework/Modules/module.private.modulemap",
+// CHECK-NEXT:         "[[PREFIX]]/frameworks/FW.framework/PrivateHeaders/FW_Private.h"
+// CHECK-NEXT:       ],
+// CHECK-NEXT:       "name": "FW_Private"
+// CHECK-NEXT:     }
+// CHECK-NEXT:   ],
+// CHECK-NEXT:   "translation-units": [
+// CHECK-NEXT:     {
+// CHECK-NEXT:       "clang-context-hash": "{{.*}}",
+// CHECK-NEXT:       "clang-module-deps": [
+// CHECK-NEXT:         {
+// CHECK-NEXT:           "context-hash": "{{.*}}",
+// CHECK-NEXT:           "module-name": "FW"
+// CHECK-NEXT:         },
+// CHECK-NEXT:         {
+// CHECK-NEXT:           "context-hash": "{{.*}}",
+// CHECK-NEXT:           "module-name": "FW_Private"
+// CHECK-NEXT:         }
+// CHECK-NEXT:       ],
+// CHECK-NEXT:       "command-line": [
+// CHECK:              "-fmodule-file={{.*}}/FW_Private-{{.*}}.pcm"
+// CHECK:              "-fmodule-file={{.*}}/FW-{{.*}}.pcm"
+// CHECK:            ],
+// CHECK-NEXT:       "file-deps": [
+// CHECK-NEXT:         "[[PREFIX]]/tu.m"
+// CHECK-NEXT:       ],
+// CHECK-NEXT:       "input-file": "[[PREFIX]]/tu.m"
+// CHECK-NEXT:     }
+// CHECK-NEXT:   ]
+// CHECK-NEXT: }
+
+// RUN: %deps-to-rsp %t/result.json --module-name=FW > %t/FW.cc1.rsp
+// RUN: %deps-to-rsp %t/result.json --module-name=FW_Private > %t/FW_Private.cc1.rsp
+// RUN: %deps-to-rsp %t/result.json --tu-index=0 > %t/tu.rsp
+// RUN: %clang @%t/FW.cc1.rsp
+// RUN: %clang @%t/FW_Private.cc1.rsp
+// RUN: %clang @%t/tu.rsp
diff --git a/clang/test/Modules/implicit-map-dot-private.m b/clang/test/Modules/implicit-map-dot-private.m
--- a/clang/test/Modules/implicit-map-dot-private.m
+++ b/clang/test/Modules/implicit-map-dot-private.m
@@ -1,5 +1,17 @@
 // RUN: rm -rf %t
-// RUN: %clang_cc1 -verify -fmodules -fimplicit-module-maps -fmodules-cache-path=%t -F %S/Inputs/implicit-private-canonical -emit-pch -o %t-A.pch %s -Wprivate-module
+
+// Implicit modules.
+// RUN: %clang_cc1 -verify -fmodules -fimplicit-module-maps -fmodules-cache-path=%t \
+// RUN:   -F %S/Inputs/implicit-private-canonical -fsyntax-only %s -Wprivate-module
+
+// Explicit modules.
+// RUN: %clang_cc1 -x objective-c -fmodules -emit-module -fmodule-name=A -o %t/A.pcm \
+// RUN:   %S/Inputs/implicit-private-canonical/A.framework/Modules/module.modulemap -Wprivate-module
+// RUN: %clang_cc1 -x objective-c -fmodules -emit-module -fmodule-name=A_Private -o %t/A_Private.pcm \
+// RUN:   %S/Inputs/implicit-private-canonical/A.framework/Modules/module.private.modulemap -Wprivate-module
+// RUN: %clang_cc1 -verify -fmodules -fimplicit-module-maps -fno-implicit-modules \
+// RUN:   -fmodule-file=A=%t/A.pcm -fmodule-file=A_Private=%t/A_Private.pcm \
+// RUN:   -F %S/Inputs/implicit-private-canonical -fsyntax-only %s -Wprivate-module
 
 #ifndef HEADER
 #define HEADER