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
@@ -46,9 +46,10 @@
   /// mismatching size of the file. If file is not minimized, the full file is
   /// read and copied into memory to ensure that it's not memory mapped to avoid
   /// running out of file descriptors.
-  static CachedFileSystemEntry createFileEntry(StringRef Filename,
-                                               llvm::vfs::FileSystem &FS,
-                                               bool Minimize = true);
+  static CachedFileSystemEntry
+  createFileEntry(StringRef Filename, llvm::vfs::FileSystem &FS,
+                  bool Minimize = true,
+                  bool PadMinimizedToOriginalSize = false);
 
   /// Create an entry that represents a directory on the filesystem.
   static CachedFileSystemEntry createDirectoryEntry(llvm::vfs::Status &&Stat);
@@ -156,6 +157,9 @@
   /// The set of files that should not be minimized.
   llvm::StringSet<> IgnoredFiles;
 
+  /// Whether to pad minimized files to the original size.
+  bool PadMinimizedToOriginalSize = false;
+
 private:
   void setCachedEntry(StringRef Filename, const CachedFileSystemEntry *Entry) {
     bool IsInserted = Cache.try_emplace(Filename, Entry).second;
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
@@ -15,8 +15,10 @@
 using namespace tooling;
 using namespace dependencies;
 
-CachedFileSystemEntry CachedFileSystemEntry::createFileEntry(
-    StringRef Filename, llvm::vfs::FileSystem &FS, bool Minimize) {
+CachedFileSystemEntry
+CachedFileSystemEntry::createFileEntry(StringRef Filename,
+                                       llvm::vfs::FileSystem &FS, bool Minimize,
+                                       bool PadMinimizedToOriginalSize) {
   // Load the file and its content from the file system.
   llvm::ErrorOr<std::unique_ptr<llvm::vfs::File>> MaybeFile =
       FS.openFileForRead(Filename);
@@ -37,7 +39,8 @@
   const auto &Buffer = *MaybeBuffer;
   SmallVector<minimize_source_to_dependency_directives::Token, 64> Tokens;
   if (!Minimize || minimizeSourceToDependencyDirectives(
-                       Buffer->getBuffer(), MinimizedFileContents, Tokens)) {
+                       Buffer->getBuffer(), MinimizedFileContents, Tokens,
+                       nullptr, SourceLocation(), PadMinimizedToOriginalSize)) {
     // Use the original file unless requested otherwise, or
     // if the minimization failed.
     // FIXME: Propage the diagnostic if desired by the client.
@@ -185,7 +188,7 @@
             std::move(*MaybeStatus));
       else
         CacheEntry = CachedFileSystemEntry::createFileEntry(
-            Filename, FS, !KeepOriginalSource);
+            Filename, FS, !KeepOriginalSource, PadMinimizedToOriginalSize);
     }
 
     Result = &CacheEntry;
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
@@ -139,6 +139,15 @@
       FileMgr->setVirtualFileSystem(createVFSFromCompilerInvocation(
           CI, Compiler.getDiagnostics(), DepFS));
 
+      // If we are about to import a PCH, make sure minimized files are padded
+      // to sizes of the originals. The PCH might have been built from
+      // non-minimized files and any disagreement on the file size causes issues
+      // in the implicit build.
+      // TODO: Consider padding only files that contributed to the PCH and its
+      // modules.
+      DepFS->PadMinimizedToOriginalSize =
+          !Compiler.getPreprocessorOpts().ImplicitPCHInclude.empty();
+
       // Pass the skip mappings which should speed up excluded conditional block
       // skipping in the preprocessor.
       if (PPSkipMappings)
diff --git a/clang/test/ClangScanDeps/modules-pch.c b/clang/test/ClangScanDeps/modules-pch.c
--- a/clang/test/ClangScanDeps/modules-pch.c
+++ b/clang/test/ClangScanDeps/modules-pch.c
@@ -6,7 +6,7 @@
 // RUN: sed "s|DIR|%/t|g" %S/Inputs/modules-pch/cdb_pch.json > %t/cdb.json
 // RUN: echo -%t > %t/result_pch.json
 // RUN: clang-scan-deps -compilation-database %t/cdb.json -format experimental-full \
-// RUN:   -generate-modules-path-args -module-files-dir %t/build -mode preprocess >> %t/result_pch.json
+// RUN:   -generate-modules-path-args -module-files-dir %t/build >> %t/result_pch.json
 // RUN: cat %t/result_pch.json | sed 's:\\\\\?:/:g' | FileCheck %s -check-prefix=CHECK-PCH
 //
 // Check we didn't build the PCH during dependency scanning.
@@ -127,9 +127,8 @@
 //
 // RUN: sed "s|DIR|%/t|g" %S/Inputs/modules-pch/cdb_tu.json > %t/cdb.json
 // RUN: echo -%t > %t/result_tu.json
-// FIXME: Make this work with '-mode preprocess-minimized-sources'.
 // RUN: clang-scan-deps -compilation-database %t/cdb.json -format experimental-full \
-// RUN:   -generate-modules-path-args -module-files-dir %t/build -mode preprocess >> %t/result_tu.json
+// RUN:   -generate-modules-path-args -module-files-dir %t/build >> %t/result_tu.json
 // RUN: cat %t/result_tu.json | sed 's:\\\\\?:/:g' | FileCheck %s -check-prefix=CHECK-TU
 //
 // CHECK-TU:      -[[PREFIX:.*]]
@@ -193,7 +192,7 @@
 // RUN: sed "s|DIR|%/t|g" %S/Inputs/modules-pch/cdb_tu_with_common.json > %t/cdb.json
 // RUN: echo -%t > %t/result_tu_with_common.json
 // RUN: clang-scan-deps -compilation-database %t/cdb.json -format experimental-full \
-// RUN:   -generate-modules-path-args -module-files-dir %t/build -mode preprocess >> %t/result_tu_with_common.json
+// RUN:   -generate-modules-path-args -module-files-dir %t/build >> %t/result_tu_with_common.json
 // RUN: cat %t/result_tu_with_common.json | sed 's:\\\\\?:/:g' | FileCheck %s -check-prefix=CHECK-TU-WITH-COMMON
 //
 // CHECK-TU-WITH-COMMON:      -[[PREFIX:.*]]