--- a/Lib/fontmake/font_project.py
+++ b/Lib/fontmake/font_project.py
@@ -149,8 +149,7 @@ class FontProject:
             os.mkdir(master_dir)
         if instance_dir is None:
             instance_dir = self._output_dir("ufo", is_instance=True)
+            instance_dir = os.path.join("..",instance_dir)
-        if not os.path.isdir(instance_dir):
-            os.mkdir(instance_dir)
 
         try:
             font = glyphsLib.GSFont(glyphs_path)