diff --git a/lisp/emacs-lisp/package.el b/lisp/emacs-lisp/package.el
index e1172d69bf0..43842cfea73 100644
--- a/lisp/emacs-lisp/package.el
+++ b/lisp/emacs-lisp/package.el
@@ -1982,7 +1982,10 @@ package--find-non-dependencies
 
 (defun package--save-selected-packages (&optional value)
   "Set and save `package-selected-packages' to VALUE."
-  (when value
+  (when (or value after-init-time)
+    ;; It is valid to set it to nil, for example when the last package
+    ;; is uninstalled.  But it shouldn't be done at init time, to
+    ;; avoid overwriting configurations that haven't yet been loaded.
     (setq package-selected-packages value))
   (if after-init-time
       (customize-save-variable 'package-selected-packages package-selected-packages)