diff --git a/infra/base-images/base-builder/indexer/clang_wrapper.py b/infra/base-images/base-builder/indexer/clang_wrapper.py
index fce81109854e..3918fac1f32b 100755
--- a/infra/base-images/base-builder/indexer/clang_wrapper.py
+++ b/infra/base-images/base-builder/indexer/clang_wrapper.py
@@ -511,6 +511,9 @@ def load_cdbs(directory: Path) -> Iterator[tuple[Path, dict[str, Any]]]:
       if file.suffix != ".json":
         continue
 
+      if file.name.endswith("_linker_commands.json"):
+        continue
+
       fragment_data = _wait_for_cdb_fragment(file)
       if not fragment_data:
         continue
diff --git a/infra/base-images/base-builder/indexer/clang_wrapper_test.py b/infra/base-images/base-builder/indexer/clang_wrapper_test.py
index 9292ccb6c9d2..07b9853829a7 100644
--- a/infra/base-images/base-builder/indexer/clang_wrapper_test.py
+++ b/infra/base-images/base-builder/indexer/clang_wrapper_test.py
@@ -86,6 +86,7 @@ def test_merge_incremental_cdb(self):
             "output": "foo.o",
             "arguments": ["-c", "foo.c"],
         },
+        "foo.123_linker_commands.json": {"invalid": "foo"},
     }
 
     new_cdb_fragments = {
@@ -98,8 +99,13 @@ def test_merge_incremental_cdb(self):
     }
 
     for cdb_fragment_path, cdb_fragment in old_cdb_fragments.items():
+      suffix = (
+          ",\n"
+          if not cdb_fragment_path.endswith("_linker_commands.json")
+          else ""
+      )
       (merged_cdb_path / cdb_fragment_path).write_text(
-          json.dumps(cdb_fragment) + ",\n"
+          json.dumps(cdb_fragment) + suffix
       )
 
     for cdb_fragment_path, cdb_fragment in new_cdb_fragments.items():
@@ -118,6 +124,7 @@ def test_merge_incremental_cdb(self):
             pathlib.Path(merged_cdb_path) / "test.c.123.json",
             pathlib.Path(merged_cdb_path) / "test.c.aaa.json",
             pathlib.Path(merged_cdb_path) / "foo.c.455.json",
+            pathlib.Path(merged_cdb_path) / "foo.123_linker_commands.json",
         ],
     )