diff --git a/lisp/org.el b/lisp/org.el
index b612e47bd..c4caed8b5 100644
--- a/lisp/org.el
+++ b/lisp/org.el
@@ -4905,10 +4905,12 @@ Support for group tags is controlled by the option
 			 (setq ret (save-match-data
 				     (org-set-regexps-and-options-for-tags)))))
 		     ;; Append setupfile tags to existing tags
-		     (setq org-file-tags (append org-file-tags (nth 0 ret))
-			   org-tag-alist (append org-tag-alist (nth 1 ret))
+		     (setq org-file-tags
+			   (delq nil (append org-file-tags (nth 0 ret)))
+			   org-tag-alist
+			   (delq nil (append org-tag-alist (nth 1 ret)))
 			   org-tag-groups-alist
-			   (append org-tag-groups-alist (nth 2 ret)))))
+			   (delq nil (append org-tag-groups-alist (nth 2 ret))))))
 		  (and ext-setup-or-nil
 		       (string-match re ext-setup-or-nil start)
 		       (setq start (match-end 0)))