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
@@ -15,6 +15,7 @@
 #include "support/Trace.h"
 #include "clang/AST/DeclTemplate.h"
 #include "clang/Basic/Diagnostic.h"
+#include "clang/Basic/DiagnosticLex.h"
 #include "clang/Basic/LangOptions.h"
 #include "clang/Basic/SourceLocation.h"
 #include "clang/Basic/SourceManager.h"
@@ -341,6 +342,20 @@
   llvm::IntrusiveRefCntPtr<DiagnosticsEngine> PreambleDiagsEngine =
       CompilerInstance::createDiagnostics(&CI.getDiagnosticOpts(),
                                           &PreambleDiagnostics, false);
+  PreambleDiagnostics.setLevelAdjuster(
+      [&](DiagnosticsEngine::Level DiagLevel, const clang::Diagnostic &Info) {
+        switch (Info.getID()) {
+        case diag::warn_no_newline_eof:
+        case diag::warn_cxx98_compat_no_newline_eof:
+        case diag::ext_no_newline_eof:
+          // If the preamble doesn't span the whole file, drop the no newline at
+          // eof warnings.
+          return Bounds.Size != ContentsBuffer->getBufferSize()
+                     ? DiagnosticsEngine::Level::Ignored
+                     : DiagLevel;
+        }
+        return DiagLevel;
+      });
 
   // Skip function bodies when building the preamble to speed up building
   // the preamble and make it smaller.
diff --git a/clang-tools-extra/clangd/unittests/DiagnosticsTests.cpp b/clang-tools-extra/clangd/unittests/DiagnosticsTests.cpp
--- a/clang-tools-extra/clangd/unittests/DiagnosticsTests.cpp
+++ b/clang-tools-extra/clangd/unittests/DiagnosticsTests.cpp
@@ -1373,6 +1373,25 @@
   EXPECT_THAT(*AST.getDiagnostics(),
               testing::Contains(Diag(Code.range(), KDiagMsg.str())));
 }
+
+TEST(Preamble, EndsOnNonEmptyLine) {
+  TestTU TU;
+  TU.ExtraArgs = {"-Wnewline-eof"};
+
+  {
+    TU.Code = "#define FOO\n  void bar();\n";
+    auto AST = TU.build();
+    EXPECT_THAT(*AST.getDiagnostics(), IsEmpty());
+  }
+  {
+    Annotations Code("#define FOO[[]]");
+    TU.Code = Code.code().str();
+    auto AST = TU.build();
+    EXPECT_THAT(
+        *AST.getDiagnostics(),
+        testing::Contains(Diag(Code.range(), "no newline at end of file")));
+  }
+}
 } // namespace
 } // namespace clangd
 } // namespace clang