diff --git a/clang-tools-extra/clangd/CompileCommands.cpp b/clang-tools-extra/clangd/CompileCommands.cpp
--- a/clang-tools-extra/clangd/CompileCommands.cpp
+++ b/clang-tools-extra/clangd/CompileCommands.cpp
@@ -208,8 +208,13 @@
   Cmd = tooling::getStripPluginsAdjuster()(Cmd, "");
   Cmd = tooling::getClangSyntaxOnlyAdjuster()(Cmd, "");
 
-  if (ResourceDir && !Has("-resource-dir"))
-    Cmd.push_back(("-resource-dir=" + *ResourceDir));
+  if (!Has("-resource-dir")) {
+    // Prefer specified resource-dir over the one in config.
+    auto RDir =
+        ResourceDir ? *ResourceDir : Config::current().CompileFlags.ResourceDir;
+    if (!RDir.empty())
+      Cmd.push_back(("-resource-dir=" + RDir));
+  }
 
   // Don't set `-isysroot` if it is already set or if `--sysroot` is set.
   // `--sysroot` is a superset of the `-isysroot` argument.
@@ -503,7 +508,6 @@
   Args.resize(Write);
 }
 
-
 std::string printArgv(llvm::ArrayRef<llvm::StringRef> Args) {
   std::string Buf;
   llvm::raw_string_ostream OS(Buf);
diff --git a/clang-tools-extra/clangd/Config.h b/clang-tools-extra/clangd/Config.h
--- a/clang-tools-extra/clangd/Config.h
+++ b/clang-tools-extra/clangd/Config.h
@@ -65,6 +65,8 @@
         Edits;
     /// Where to search for compilation databases for this file's flags.
     CDBSearchSpec CDBSearch = {CDBSearchSpec::Ancestors, llvm::None};
+    /// Directory to look for internal headers.
+    std::string ResourceDir;
   } CompileFlags;
 
   enum class BackgroundPolicy { Build, Skip };
diff --git a/clang-tools-extra/clangd/ConfigCompile.cpp b/clang-tools-extra/clangd/ConfigCompile.cpp
--- a/clang-tools-extra/clangd/ConfigCompile.cpp
+++ b/clang-tools-extra/clangd/ConfigCompile.cpp
@@ -301,6 +301,16 @@
               C.CompileFlags.CDBSearch = Spec;
             });
     }
+
+    if (F.ResourceDir) {
+      if (auto Path = makeAbsolute(*F.ResourceDir, "ResourceDir",
+                                   llvm::sys::path::Style::native)) {
+        Out.Apply.push_back(
+            [Path(std::move(*Path))](const Params &, Config &C) {
+              C.CompileFlags.ResourceDir = Path;
+            });
+      }
+    }
   }
 
   void compile(Fragment::IndexBlock &&F) {
diff --git a/clang-tools-extra/clangd/ConfigFragment.h b/clang-tools-extra/clangd/ConfigFragment.h
--- a/clang-tools-extra/clangd/ConfigFragment.h
+++ b/clang-tools-extra/clangd/ConfigFragment.h
@@ -158,6 +158,11 @@
     /// - Ancestors: search all parent directories (the default)
     /// - None: do not use a compilation database, just default flags.
     llvm::Optional<Located<std::string>> CompilationDatabase;
+
+    /// Path to a directory on user's machine, that'll be used to search for
+    /// built-in headers. Relative paths may be used, if config fragment is
+    /// associated with a directory.
+    llvm::Optional<Located<std::string>> ResourceDir;
   };
   CompileFlagsBlock CompileFlags;
 
diff --git a/clang-tools-extra/clangd/ConfigYAML.cpp b/clang-tools-extra/clangd/ConfigYAML.cpp
--- a/clang-tools-extra/clangd/ConfigYAML.cpp
+++ b/clang-tools-extra/clangd/ConfigYAML.cpp
@@ -98,6 +98,9 @@
     Dict.handle("CompilationDatabase", [&](Node &N) {
       F.CompilationDatabase = scalarValue(N, "CompilationDatabase");
     });
+    Dict.handle("ResourceDir", [&](Node &N) {
+      F.ResourceDir = scalarValue(N, "ResourceDir");
+    });
     Dict.parse(N);
   }
 
diff --git a/clang-tools-extra/clangd/unittests/CompileCommandsTests.cpp b/clang-tools-extra/clangd/unittests/CompileCommandsTests.cpp
--- a/clang-tools-extra/clangd/unittests/CompileCommandsTests.cpp
+++ b/clang-tools-extra/clangd/unittests/CompileCommandsTests.cpp
@@ -52,10 +52,22 @@
 
 TEST(CommandMangler, ResourceDir) {
   auto Mangler = CommandMangler::forTests();
-  Mangler.ResourceDir = testPath("fake/resources");
+
+  // Check config works.
+  Config Cfg;
+  auto ResourceDir = testPath("config/resources");
+  Cfg.CompileFlags.ResourceDir = ResourceDir;
+  WithContextValue WithConfig(Config::Key, std::move(Cfg));
   std::vector<std::string> Cmd = {"clang++", "foo.cc"};
   Mangler.adjust(Cmd);
-  EXPECT_THAT(Cmd, Contains("-resource-dir=" + testPath("fake/resources")));
+  EXPECT_THAT(Cmd, Contains("-resource-dir=" + ResourceDir));
+
+  // Check that explicit option overrides config.
+  ResourceDir = testPath("explicit/resources");
+  Mangler.ResourceDir = ResourceDir;
+  Cmd = {"clang++", "foo.cc"};
+  Mangler.adjust(Cmd);
+  EXPECT_THAT(Cmd, Contains("-resource-dir=" + ResourceDir));
 }
 
 TEST(CommandMangler, Sysroot) {
@@ -378,4 +390,3 @@
 } // namespace
 } // namespace clangd
 } // namespace clang
-
diff --git a/clang-tools-extra/clangd/unittests/ConfigCompileTests.cpp b/clang-tools-extra/clangd/unittests/ConfigCompileTests.cpp
--- a/clang-tools-extra/clangd/unittests/ConfigCompileTests.cpp
+++ b/clang-tools-extra/clangd/unittests/ConfigCompileTests.cpp
@@ -171,6 +171,22 @@
   EXPECT_THAT(Diags.Diagnostics, IsEmpty());
 }
 
+TEST_F(ConfigCompileTests, ResourceDir) {
+  EXPECT_TRUE(compileAndApply());
+  EXPECT_TRUE(Conf.CompileFlags.ResourceDir.empty());
+
+  auto ResourceDir = testPath("foo");
+  Frag.CompileFlags.ResourceDir.emplace(ResourceDir);
+  EXPECT_TRUE(compileAndApply());
+  EXPECT_EQ(Conf.CompileFlags.ResourceDir, ResourceDir);
+
+  ResourceDir = "foo";
+  Frag.Source.Directory = testRoot();
+  Frag.CompileFlags.ResourceDir.emplace(ResourceDir);
+  EXPECT_TRUE(compileAndApply());
+  EXPECT_EQ(Conf.CompileFlags.ResourceDir, testPath("foo"));
+}
+
 TEST_F(ConfigCompileTests, Index) {
   Frag.Index.Background.emplace("Skip");
   EXPECT_TRUE(compileAndApply());
diff --git a/clang-tools-extra/clangd/unittests/ConfigYAMLTests.cpp b/clang-tools-extra/clangd/unittests/ConfigYAMLTests.cpp
--- a/clang-tools-extra/clangd/unittests/ConfigYAMLTests.cpp
+++ b/clang-tools-extra/clangd/unittests/ConfigYAMLTests.cpp
@@ -14,6 +14,7 @@
 #include "llvm/Support/SMLoc.h"
 #include "llvm/Support/ScopedPrinter.h"
 #include "llvm/Support/SourceMgr.h"
+#include "llvm/Testing/Support/SupportHelpers.h"
 #include "gmock/gmock.h"
 #include "gtest/gtest.h"
 
@@ -164,6 +165,17 @@
   EXPECT_THAT(*Results[0].Index.External.getValue()->Server, Val("bar"));
 }
 
+TEST(ParseYAML, ResourceDir) {
+  CapturedDiags Diags;
+  Annotations YAML(R"yaml(
+CompileFlags:
+  ResourceDir: "foo")yaml");
+  auto Results =
+      Fragment::parseYAML(YAML.code(), "config.yaml", Diags.callback());
+  ASSERT_EQ(Results.size(), 1u);
+  ASSERT_THAT(Diags.Diagnostics, IsEmpty());
+  EXPECT_THAT(Results[0].CompileFlags.ResourceDir, llvm::ValueIs(Val("foo")));
+}
 } // namespace
 } // namespace config
 } // namespace clangd