Index: clangd/index/SymbolCollector.cpp
===================================================================
--- clangd/index/SymbolCollector.cpp
+++ clangd/index/SymbolCollector.cpp
@@ -345,16 +345,20 @@
       SM.getFileID(SpellingLoc) == SM.getMainFileID())
     ReferencedDecls.insert(ND);
 
-  if ((static_cast<unsigned>(Opts.RefFilter) & Roles) &&
-      SM.getFileID(SpellingLoc) == SM.getMainFileID())
-    DeclRefs[ND].emplace_back(SpellingLoc, Roles);
+  bool CollectRef = static_cast<unsigned>(Opts.RefFilter) & Roles;
+  bool IsOnlyRef =
+      !(Roles & (static_cast<unsigned>(index::SymbolRole::Declaration) |
+                 static_cast<unsigned>(index::SymbolRole::Definition)));
 
-  // Don't continue indexing if this is a mere reference.
-  if (!(Roles & static_cast<unsigned>(index::SymbolRole::Declaration) ||
-        Roles & static_cast<unsigned>(index::SymbolRole::Definition)))
+  if (IsOnlyRef && !CollectRef)
     return true;
   if (!shouldCollectSymbol(*ND, *ASTCtx, Opts))
     return true;
+  if (CollectRef && SM.getFileID(SpellingLoc) == SM.getMainFileID())
+    DeclRefs[ND].emplace_back(SpellingLoc, Roles);
+  // Don't continue indexing if this is a mere reference.
+  if (IsOnlyRef)
+    return true;
 
   auto ID = getSymbolID(ND);
   if (!ID)
@@ -476,17 +480,15 @@
     std::string MainURI = *MainFileURI;
     for (const auto &It : DeclRefs) {
       if (auto ID = getSymbolID(It.first)) {
-        if (Symbols.find(*ID)) {
-          for (const auto &LocAndRole : It.second) {
-            Ref R;
-            auto Range =
-                getTokenRange(LocAndRole.first, SM, ASTCtx->getLangOpts());
-            R.Location.Start = Range.first;
-            R.Location.End = Range.second;
-            R.Location.FileURI = MainURI;
-            R.Kind = toRefKind(LocAndRole.second);
-            Refs.insert(*ID, R);
-          }
+        for (const auto &LocAndRole : It.second) {
+          Ref R;
+          auto Range =
+              getTokenRange(LocAndRole.first, SM, ASTCtx->getLangOpts());
+          R.Location.Start = Range.first;
+          R.Location.End = Range.second;
+          R.Location.FileURI = MainURI;
+          R.Kind = toRefKind(LocAndRole.second);
+          Refs.insert(*ID, R);
         }
       }
     }
Index: unittests/clangd/FileIndexTests.cpp
===================================================================
--- unittests/clangd/FileIndexTests.cpp
+++ unittests/clangd/FileIndexTests.cpp
@@ -8,6 +8,7 @@
 //===----------------------------------------------------------------------===//
 
 #include "Annotations.h"
+#include "AST.h"
 #include "ClangdUnit.h"
 #include "TestFS.h"
 #include "TestTU.h"
@@ -15,6 +16,7 @@
 #include "index/FileIndex.h"
 #include "clang/Frontend/CompilerInvocation.h"
 #include "clang/Frontend/PCHContainerOperations.h"
+#include "clang/Frontend/Utils.h"
 #include "clang/Index/IndexSymbol.h"
 #include "clang/Lex/Preprocessor.h"
 #include "clang/Tooling/CompilationDatabase.h"
@@ -346,6 +348,55 @@
   EXPECT_TRUE(SeenSymbol);
 }
 
+TEST(FileIndexTest, ReferencesInMainFileWithPreamble) {
+  const std::string Header = R"cpp(
+    class Foo {};
+  )cpp";
+  Annotations Main(R"cpp(
+    #include "foo.h"
+    void f() {
+      [[Foo]] foo;
+    }
+  )cpp");
+  auto MainFile = testPath("foo.cpp");
+  auto HeaderFile = testPath("foo.h");
+  std::vector<const char*> Cmd = {"clang", "-xc++", MainFile.c_str()};
+  // Preparse ParseInputs.
+  ParseInputs PI;
+  PI.CompileCommand.Directory = testRoot();
+  PI.CompileCommand.Filename = MainFile;
+  PI.CompileCommand.CommandLine = {Cmd.begin(), Cmd.end()};
+  PI.Contents = Main.code();
+  PI.FS = buildTestFS({{MainFile, Main.code()}, {HeaderFile, Header}});
+
+  // Prepare preamble.
+  auto CI = buildCompilerInvocation(PI);
+  auto PreambleData = buildPreamble(
+      MainFile,
+      *buildCompilerInvocation(PI), /*OldPreamble=*/nullptr,
+      tooling::CompileCommand(), PI,
+      std::make_shared<PCHContainerOperations>(), /*StoreInMemory=*/true,
+      [&](ASTContext &Ctx, std::shared_ptr<Preprocessor> PP) {});
+  // Build AST for main file with preamble.
+  auto AST = ParsedAST::build(
+      createInvocationFromCommandLine(Cmd), PreambleData,
+      llvm::MemoryBuffer::getMemBufferCopy(Main.code()),
+      std::make_shared<PCHContainerOperations>(),
+      PI.FS);
+  ASSERT_TRUE(AST);
+  FileIndex Index;
+  Index.updateMain(MainFile, *AST);
+
+  auto Foo =
+      findSymbol(TestTU::withHeaderCode(Header).headerSymbols(), "Foo");
+  RefsRequest Request;
+  Request.IDs.insert(Foo.ID);
+
+  // Expect to see references in main file, references in headers are excluded
+  // because we only index main AST.
+  EXPECT_THAT(getRefs(Index, Foo.ID), RefsAre({RefRange(Main.range())}));
+}
+
 } // namespace
 } // namespace clangd
 } // namespace clang