diff --git a/ci/do_ci.sh b/ci/do_ci.sh
index 2341bd0f9b40c..43aa3f7a1ffd6 100755
--- a/ci/do_ci.sh
+++ b/ci/do_ci.sh
@@ -1041,15 +1041,24 @@ case $CI_TARGET in
         ;;
 
     refresh_compdb)
+        # Override the BAZEL_STARTUP_OPTIONS to setting different output directory.
+        # So the compdb headers won't be overwritten by another bazel run.
+        for i in "${!BAZEL_STARTUP_OPTIONS[@]}"; do
+            if [[ ${BAZEL_STARTUP_OPTIONS[i]} == "--output_base"* ]]; then
+                COMPDB_OUTPUT_BASE="${BAZEL_STARTUP_OPTIONS[i]}"-envoy-compdb
+                BAZEL_STARTUP_OPTIONS[i]="${COMPDB_OUTPUT_BASE}"
+                BAZEL_STARTUP_OPTION_LIST="${BAZEL_STARTUP_OPTIONS[*]}"
+                export BAZEL_STARTUP_OPTION_LIST
+            fi
+        done
+
         if [[ -z "${SKIP_PROTO_FORMAT}" ]]; then
             "${CURRENT_SCRIPT_DIR}/../tools/proto_format/proto_format.sh" fix
         fi
 
         read -ra ENVOY_GEN_COMPDB_OPTIONS <<< "${ENVOY_GEN_COMPDB_OPTIONS:-}"
 
-        # Setting TEST_TMPDIR here so the compdb headers won't be overwritten by another bazel run.
-        TEST_TMPDIR="${BUILD_DIR}/envoy-compdb" \
-            "${CURRENT_SCRIPT_DIR}/../tools/gen_compilation_database.py" \
+        "${CURRENT_SCRIPT_DIR}/../tools/gen_compilation_database.py" \
             "${ENVOY_GEN_COMPDB_OPTIONS[@]}"
         # Kill clangd to reload the compilation database
         pkill clangd || :
diff --git a/tools/gen_compilation_database.py b/tools/gen_compilation_database.py
index 2dfdaa79fd175..8153c1ad30b2c 100755
--- a/tools/gen_compilation_database.py
+++ b/tools/gen_compilation_database.py
@@ -28,8 +28,8 @@ def generate_compilation_database(args):
     ] + source_dir_targets)
 
     execroot = subprocess.check_output(
-        ["bazel", *bazel_startup_options, "info", *bazel_options, "execution_root",
-         *bazel_options]).decode().strip()
+        ["bazel", *bazel_startup_options, "info", *bazel_options,
+         "execution_root"]).decode().strip()
 
     db_entries = []
     for db in Path(execroot).glob('**/*.compile_commands.json'):