diff --git a/tools/run_tests/run_microbenchmark.py b/tools/run_tests/run_microbenchmark.py
index 4ee34957e4a81af4721d02bfbd41173ba2ba3998..f72ec72dcedf755d36fe82cb388dc22ef57b5ccd 100755
--- a/tools/run_tests/run_microbenchmark.py
+++ b/tools/run_tests/run_microbenchmark.py
@@ -238,6 +238,7 @@ if args.diff_perf:
   where_am_i = subprocess.check_call(['git', 'rev-parse', '--abbrev-ref', 'HEAD'])
   subprocess.check_call(['git', 'checkout', args.diff_perf])
   comparables = []
+  subprocess.check_call(['make', 'clean'])
   try:
     for bm_name in args.benchmarks:
       try: