diff --git a/lisp/emacs-lisp/package.el b/lisp/emacs-lisp/package.el
index e1172d69bf0..6d0ad274795 100644
--- a/lisp/emacs-lisp/package.el
+++ b/lisp/emacs-lisp/package.el
@@ -1982,8 +1982,11 @@ package--find-non-dependencies
 
 (defun package--save-selected-packages (&optional value)
   "Set and save `package-selected-packages' to VALUE."
-  (when value
-    (setq package-selected-packages value))
+  (cond
+   ((eq value 'empty)
+    (setq package-selected-packages nil))
+   ((not (null package-selected-packages))
+    (setq package-selected-packages value)))
   (if after-init-time
       (customize-save-variable 'package-selected-packages package-selected-packages)
     (add-hook 'after-init-hook #'package--save-selected-packages)))
@@ -2527,7 +2530,7 @@ package-delete
                ;; Don't deselect if this is an older version of an
                ;; upgraded package.
                (package--newest-p pkg-desc))
-      (package--save-selected-packages (remove name package-selected-packages)))
+      (package--save-selected-packages (or (remove name package-selected-packages) 'empty)))
     (cond ((not (string-prefix-p (file-name-as-directory
                                   (expand-file-name package-user-dir))
                                  (expand-file-name dir)))