diff --git a/clang-tools-extra/clangd/Preamble.cpp b/clang-tools-extra/clangd/Preamble.cpp
--- a/clang-tools-extra/clangd/Preamble.cpp
+++ b/clang-tools-extra/clangd/Preamble.cpp
@@ -671,10 +671,10 @@
     // We are only interested in newly added includes, record the ones in
     // Baseline for exclusion.
     llvm::DenseMap<std::pair<tok::PPKeywordKind, llvm::StringRef>,
-                   /*Resolved=*/llvm::StringRef>
+                   const Inclusion *>
         ExistingIncludes;
     for (const auto &Inc : Baseline.Includes.MainFileIncludes)
-      ExistingIncludes[{Inc.Directive, Inc.Written}] = Inc.Resolved;
+      ExistingIncludes[{Inc.Directive, Inc.Written}] = &Inc;
     // There might be includes coming from disabled regions, record these for
     // exclusion too. note that we don't have resolved paths for those.
     for (const auto &Inc : BaselineScan->Includes)
@@ -685,7 +685,14 @@
       // Include already present in the baseline preamble. Set resolved path and
       // put into preamble includes.
       if (It != ExistingIncludes.end()) {
-        Inc.Resolved = It->second.str();
+        // Copy everything from existing include, apart from the location, when
+        // it's coming from baseline preamble.
+        if (It->second) {
+          Inc.Resolved = It->second->Resolved;
+          Inc.HeaderID = It->second->HeaderID;
+          Inc.BehindPragmaKeep = It->second->BehindPragmaKeep;
+          Inc.FileKind = It->second->FileKind;
+        }
         PP.PreambleIncludes.push_back(Inc);
         continue;
       }
@@ -696,6 +703,10 @@
       Patch << llvm::formatv(
           "#{0} {1}\n", spellingForIncDirective(Inc.Directive), Inc.Written);
     }
+  } else {
+    // Includes haven't changed or we're not patching.
+    // So, copy them over from the baseline.
+    PP.PreambleIncludes = Baseline.Includes.MainFileIncludes;
   }
 
   if (DirectivesChanged) {
diff --git a/clang-tools-extra/clangd/unittests/PreambleTests.cpp b/clang-tools-extra/clangd/unittests/PreambleTests.cpp
--- a/clang-tools-extra/clangd/unittests/PreambleTests.cpp
+++ b/clang-tools-extra/clangd/unittests/PreambleTests.cpp
@@ -15,6 +15,7 @@
 #include "TestFS.h"
 #include "TestTU.h"
 #include "XRefs.h"
+#include "clang/Basic/SourceManager.h"
 #include "clang/Format/Format.h"
 #include "clang/Frontend/FrontendActions.h"
 #include "clang/Frontend/PrecompiledPreamble.h"
@@ -23,6 +24,7 @@
 #include "llvm/Support/MemoryBuffer.h"
 #include "llvm/Support/VirtualFileSystem.h"
 #include "gmock/gmock.h"
+#include "gtest/gtest-matchers.h"
 #include "gtest/gtest.h"
 #include <memory>
 #include <optional>
@@ -166,7 +168,7 @@
   MockFS FS;
   IgnoreDiagnostics Diags;
   auto TU = TestTU::withCode(R"cpp(
-    #include "a.h"
+    #include "a.h" // IWYU pragma: keep
     #include "c.h"
   )cpp");
   TU.AdditionalFiles["a.h"] = "#include \"b.h\"";
@@ -185,9 +187,14 @@
                                            *BaselinePreamble);
   // Only a.h should exists in the preamble, as c.h has been dropped and b.h was
   // newly introduced.
-  EXPECT_THAT(PP.preambleIncludes(),
-              ElementsAre(AllOf(Field(&Inclusion::Written, "\"a.h\""),
-                                Field(&Inclusion::Resolved, testPath("a.h")))));
+  EXPECT_THAT(
+      PP.preambleIncludes(),
+      ElementsAre(AllOf(
+          Field(&Inclusion::Written, "\"a.h\""),
+          Field(&Inclusion::Resolved, testPath("a.h")),
+          Field(&Inclusion::HeaderID, testing::Not(testing::Eq(std::nullopt))),
+          Field(&Inclusion::BehindPragmaKeep, true),
+          Field(&Inclusion::FileKind, SrcMgr::CharacteristicKind::C_User))));
 }
 
 std::optional<ParsedAST> createPatchedAST(llvm::StringRef Baseline,
@@ -225,6 +232,20 @@
       .str();
 }
 
+TEST(PreamblePatchTest, IncludesArePreserved) {
+  llvm::StringLiteral Baseline = "//error-ok\n#include <foo>\n#include <bar>\n";
+  auto Modified = Baseline + "#define FOO\n";
+
+  auto Includes = createPatchedAST(Baseline, Modified.str())
+                      ->getIncludeStructure()
+                      .MainFileIncludes;
+  EXPECT_TRUE(!Includes.empty());
+  EXPECT_EQ(Includes, TestTU::withCode(Baseline)
+                          .build()
+                          .getIncludeStructure()
+                          .MainFileIncludes);
+}
+
 TEST(PreamblePatchTest, Define) {
   // BAR should be defined while parsing the AST.
   struct {