diff --git a/src/code_checker.bzl b/src/code_checker.bzl
index 2d0c81b4..1f0d0424 100644
--- a/src/code_checker.bzl
+++ b/src/code_checker.bzl
@@ -62,7 +62,13 @@ def _run_code_checker(
     clangsa_plist = ctx.actions.declare_file(clangsa_plist_file_name)
     codechecker_log = ctx.actions.declare_file(codechecker_log_file_name)
 
-    inputs = [compile_commands_json] + sources_and_headers
+    if "--ctu" in options:
+        inputs = [compile_commands_json] + sources_and_headers
+    else:
+        # NOTE: we collect only headers, so CTU may not work!
+        headers = depset([src], transitive = [compilation_context.headers])
+        inputs = depset([compile_commands_json, src], transitive = [headers])
+
     outputs = [clang_tidy_plist, clangsa_plist, codechecker_log]
 
     # Create CodeChecker wrapper script
@@ -274,6 +280,7 @@ def _compile_commands_impl(ctx):
     return compile_commands_json
 
 def _collect_all_sources_and_headers(ctx):
+    # NOTE: we are only using this function for CTU
     all_files = []
     headers = depset()
     for target in ctx.attr.targets:
diff --git a/test/unit/caching/test_caching.py b/test/unit/caching/test_caching.py
index 4690f06b..de6e4b30 100644
--- a/test/unit/caching/test_caching.py
+++ b/test/unit/caching/test_caching.py
@@ -73,10 +73,8 @@ def test_bazel_test_code_checker_caching(self):
             self.fail(f"File not found!")
         ret, _, stderr = self.run_command(f"bazel build {target} --subcommands")
         self.assertEqual(ret, 0)
-        # FIXME: This should be 1; 2 means that both .cpp files were reanalyzed
-        # despite only one of them being changed.
         self.assertEqual(
-            stderr.count(f"SUBCOMMAND: # {target} [action 'CodeChecker"), 2
+            stderr.count(f"SUBCOMMAND: # {target} [action 'CodeChecker"), 1
         )
 
     def test_bazel_test_code_checker_ctu_caching(self):