diff --git a/clang-tools-extra/clangd/index/SymbolCollector.cpp b/clang-tools-extra/clangd/index/SymbolCollector.cpp
--- a/clang-tools-extra/clangd/index/SymbolCollector.cpp
+++ b/clang-tools-extra/clangd/index/SymbolCollector.cpp
@@ -256,6 +256,9 @@
   assert(ASTCtx && PP.get() && "ASTContext and Preprocessor must be set.");
   assert(CompletionAllocator && CompletionTUInfo);
   assert(ASTNode.OrigD);
+  auto &SM = ASTCtx->getSourceManager();
+  if (!shouldIndexFile(SM.getFileID(Loc)))
+    return true;
   // Indexing API puts canonical decl into D, which might not have a valid
   // source location for implicit/built-in decls. Fallback to original decl in
   // such cases.
@@ -298,7 +301,6 @@
 
   // Mark D as referenced if this is a reference coming from the main file.
   // D may not be an interesting symbol, but it's cheaper to check at the end.
-  auto &SM = ASTCtx->getSourceManager();
   if (Opts.CountReferences &&
       (Roles & static_cast<unsigned>(index::SymbolRole::Reference)) &&
       SM.getFileID(SM.getSpellingLoc(Loc)) == SM.getMainFileID())
@@ -405,6 +407,9 @@
     return true;
 
   const auto &SM = PP->getSourceManager();
+  if (!shouldIndexFile(SM.getFileID(Loc)))
+    return true;
+
   auto DefLoc = MI->getDefinitionLoc();
   // Also avoid storing predefined macros like __DBL_MIN__.
   if (SM.isWrittenInBuiltinFile(DefLoc))