diff --git a/flax/testing/benchmark.py b/flax/testing/benchmark.py
index ea55db31b..a45759877 100644
--- a/flax/testing/benchmark.py
+++ b/flax/testing/benchmark.py
@@ -42,13 +42,10 @@
 
 from flax import io
 
-flags.DEFINE_string(
+_BENCHMARK_OUTPUT_DIR = flags.DEFINE_string(
   'benchmark_output_dir', default=None, help='Benchmark output directory.'
 )
 
-
-FLAGS = flags.FLAGS
-
 _SCALAR_PLUGIN_NAME = (
   summary_lib.scalar_pb('', 0).value[0].metadata.plugin_data.plugin_name
 )
@@ -125,9 +122,10 @@ def __init__(self, *args, **kwargs):
         patched_func = functools.partial(self._collect_assert_wrapper, fn=func)
         setattr(self, func_name, patched_func)
 
+    self._benchmark_output_dir = _BENCHMARK_OUTPUT_DIR.value
     # Create target directory if defined.
-    if FLAGS.benchmark_output_dir and not io.exists(FLAGS.benchmark_output_dir):
-      io.makedirs(FLAGS.benchmark_output_dir)
+    if self._benchmark_output_dir and not io.exists(self._benchmark_output_dir):
+      io.makedirs(self._benchmark_output_dir)
 
   # pylint: disable=invalid-name
   def _collect_assert_wrapper(self, *args, fn=None, **kwargs):
@@ -160,8 +158,8 @@ def get_tmp_model_dir(self):
     if defined else uses a temporary directory. This helps to export summary
     files to tensorboard as multiple separate runs for each test method.
     """
-    if FLAGS.benchmark_output_dir:
-      model_dir = FLAGS.benchmark_output_dir
+    if self._benchmark_output_dir:
+      model_dir = self._benchmark_output_dir
     else:
       model_dir = tempfile.mkdtemp()
     model_dir_path = os.path.join(
@@ -281,8 +279,7 @@ def _report_benchmark_results(self):
     logging.info(results_str)
 
     # Maybe save results as a file for pickup by CI / monitoring frameworks.
-    benchmark_output_dir = FLAGS.benchmark_output_dir
-    if benchmark_output_dir:
-      filename = os.path.join(benchmark_output_dir, name + '.json')
+    if self._benchmark_output_dir:
+      filename = os.path.join(self._benchmark_output_dir, name + '.json')
       with io.GFile(filename, 'w') as fout:
         fout.write(results_str)