diff --git a/notmuch-setup.c b/notmuch-setup.c
index 9f37e4a6..c3ea9371 100644
--- a/notmuch-setup.c
+++ b/notmuch-setup.c
@@ -195,16 +195,6 @@ notmuch_setup_command (unused (void *ctx),
 	g_ptr_array_free (tags, TRUE);
     }
 
-    prompt ("Synchronize maildir flags with notmuch tags? %s: ",
-	    notmuch_config_get_maildir_synchronize_flags (config) == TRUE ? "[yes]/no" : "[no]/yes");
-    if (strlen (response) > 0) {
-	if (strcasecmp (response, "yes") == 0||
-	    strcasecmp (response, "y") == 0)
-	    notmuch_config_set_maildir_synchronize_flags (config, TRUE);
-	else
-	    notmuch_config_set_maildir_synchronize_flags (config, FALSE);
-    }
-
     if (! notmuch_config_save (config)) {
 	if (is_new)
 	  welcome_message_post_setup ();