diff --git a/cwltool/builder.py b/cwltool/builder.py
index b3a3d1d10..8a3797af7 100644
--- a/cwltool/builder.py
+++ b/cwltool/builder.py
@@ -230,7 +230,7 @@ def generate_arg(self, binding):  # type: (Dict[Text,Any]) -> List[Text]
             return [prefix] if prefix else []
         elif value is True and prefix:
             return [prefix]
-        elif value is False or value is None:
+        elif value is False or value is None or (value is True and not prefix):
             return []
         else:
             l = [value]