diff --git a/clang-tools-extra/clangd/refactor/tweaks/AnnotateHighlightings.cpp b/clang-tools-extra/clangd/refactor/tweaks/AnnotateHighlightings.cpp
--- a/clang-tools-extra/clangd/refactor/tweaks/AnnotateHighlightings.cpp
+++ b/clang-tools-extra/clangd/refactor/tweaks/AnnotateHighlightings.cpp
@@ -24,6 +24,7 @@
   const char *id() const override final;
 
   bool prepare(const Selection &Inputs) override {
+    InterestedDecl = Inputs.ASTSelection.root().ASTNode.get<Decl>();
     for (auto N = Inputs.ASTSelection.commonAncestor(); N && !InterestedDecl;
          N = N->Parent)
       InterestedDecl = N->ASTNode.get<Decl>();
@@ -41,15 +42,22 @@
 REGISTER_TWEAK(AnnotateHighlightings)
 
 Expected<Tweak::Effect> AnnotateHighlightings::apply(const Selection &Inputs) {
-  // Store the existing scopes.
-  const auto &BackupScopes = Inputs.AST.getASTContext().getTraversalScope();
-  // Narrow the traversal scope to the selected node.
-  Inputs.AST.getASTContext().setTraversalScope(
-      {const_cast<Decl *>(InterestedDecl)});
-  auto HighlightingTokens = getSemanticHighlightings(Inputs.AST);
-  // Restore the traversal scope.
-  Inputs.AST.getASTContext().setTraversalScope(BackupScopes);
-
+  std::vector<HighlightingToken> HighlightingTokens;
+  if (llvm::isa<TranslationUnitDecl>(InterestedDecl)) {
+    // We only annotate tokens in the main file, if InterestedDecl is a TUDecl,
+    // we use the default traversal scope (which is the top level decls of the
+    // main file).
+    HighlightingTokens = getSemanticHighlightings(Inputs.AST);
+  } else {
+    // Store the existing scopes.
+    const auto &BackupScopes = Inputs.AST.getASTContext().getTraversalScope();
+    // Narrow the traversal scope to the selected node.
+    Inputs.AST.getASTContext().setTraversalScope(
+        {const_cast<Decl *>(InterestedDecl)});
+    HighlightingTokens = getSemanticHighlightings(Inputs.AST);
+    // Restore the traversal scope.
+    Inputs.AST.getASTContext().setTraversalScope(BackupScopes);
+  }
   auto &SM = Inputs.AST.getSourceManager();
   tooling::Replacements Result;
   for (const auto &Token : HighlightingTokens) {
diff --git a/clang-tools-extra/clangd/unittests/TweakTests.cpp b/clang-tools-extra/clangd/unittests/TweakTests.cpp
--- a/clang-tools-extra/clangd/unittests/TweakTests.cpp
+++ b/clang-tools-extra/clangd/unittests/TweakTests.cpp
@@ -487,6 +487,7 @@
 TEST(TweakTest, AnnotateHighlightings) {
   llvm::StringLiteral ID = "AnnotateHighlightings";
   checkAvailable(ID, "^vo^id^ ^f(^) {^}^"); // available everywhere.
+  checkAvailable(ID, "[[int a; int b;]]");
   const char *Input = "void ^f() {}";
   const char *Output = "void /* entity.name.function.cpp */f() {}";
   checkTransform(ID, Input, Output);