diff --git a/pre-upload.py b/pre-upload.py
index 2ef303f..3bd6f66 100755
--- a/pre-upload.py
+++ b/pre-upload.py
@@ -698,6 +698,17 @@
                for path in contents if path.endswith('.ebuild')]
     ebuilds_9999 = [path for path in ebuilds if path.endswith('-9999.ebuild')]
 
+    affected_paths_under_9999_ebuilds = set()
+    for affected_path in affected_paths:
+      for ebuild_9999 in ebuilds_9999:
+        ebuild_dir = os.path.dirname(ebuild_9999)
+        if affected_path.startswith(ebuild_dir):
+          affected_paths_under_9999_ebuilds.add(affected_path)
+
+    # If every file changed exists under a 9999 ebuild, then skip
+    if len(affected_paths_under_9999_ebuilds) == len(affected_paths):
+      continue
+
     # If the -9999.ebuild file was touched the bot will uprev for us.
     # ...we'll use a simple intersection here as a heuristic...
     if set(ebuilds_9999) & affected_paths:
diff --git a/pre-upload_unittest.py b/pre-upload_unittest.py
index 6e517d2..f212eac 100755
--- a/pre-upload_unittest.py
+++ b/pre-upload_unittest.py
@@ -1248,6 +1248,13 @@
     self.assertAccepted([DiffEntry(src_file='c/p/files/f', status='M'),
                          DiffEntry(src_file='c/p/p-9999.ebuild', status='M')])
 
+  def testModifiedFilesIn9999SubDirWithout9999Change(self):
+    """Accept changes in files/ with a parent 9999 ebuild"""
+    ebuild_9999_file = os.path.join(self.tempdir, 'c/p/p-9999.ebuild')
+    os.makedirs(os.path.dirname(ebuild_9999_file))
+    osutils.WriteFile(ebuild_9999_file, 'fake')
+    self.assertAccepted([DiffEntry(src_file='c/p/files/f', status='M')])
+
 
 class DirectMainTest(cros_test_lib.MockTempDirTestCase):
   """Tests for direct_main()"""