diff --git a/legendary/cli.py b/legendary/cli.py
index 4093b1f..da98c8a 100644
--- a/legendary/cli.py
+++ b/legendary/cli.py
@@ -1294,10 +1294,10 @@ def main():
         logging.getLogger('requests').setLevel(logging.WARNING)
         logging.getLogger('urllib3').setLevel(logging.WARNING)
 
-    # -y having to be specified before the subcommand is a little counter-intuitive
-    # For now show a warning if a user is misusing that flag
+    # if --yes is used as part of the subparsers arguments manually set the flag in the main parser.
     if '-y' in extra or '--yes' in extra:
-        logger.warning('-y/--yes flag needs to be specified *before* the command name')
+        args.yes = True
+        extra = [i for i in extra if i not in ('--yes', '-y')]
 
     # technically args.func() with setdefaults could work (see docs on subparsers)
     # but that would require all funcs to accept args and extra...