diff --git a/lisp/org-persist.el b/lisp/org-persist.el
index 80ecd8588..f9ad26692 100644
--- a/lisp/org-persist.el
+++ b/lisp/org-persist.el
@@ -874,15 +874,21 @@ When IGNORE-RETURN is non-nil, just return t on success without calling
 When ASSOCIATED is non-nil, only save the matching data."
   (unless org-persist--index (org-persist--load-index))
   (setq associated (org-persist--normalize-associated associated))
-  (unless
+  (if
       (and (equal 1 (length org-persist--index))
            ;; The single collection only contains a single container
            ;; in the container list.
            (equal 1 (length (plist-get (car org-persist--index) :container)))
            ;; The container is an `index' container.
            (eq 'index (caar (plist-get (car org-persist--index) :container)))
-           ;; No `org-persist-directory' exists yet.
-           (not (file-exists-p org-persist-directory)))
+           (or (not (file-exists-p org-persist-directory))
+               (org-directory-empty-p org-persist-directory)))
+      ;; Do not write anything, and clear up `org-persist-directory' to reduce
+      ;; clutter.
+      (when (and (file-exists-p org-persist-directory)
+                 (org-directory-empty-p org-persist-directory))
+        (delete-directory org-persist-directory))
+    ;; Write the data.
     (let (all-containers)
       (dolist (collection org-persist--index)
         (if associated
@@ -963,19 +969,20 @@ Also, remove containers associated with non-existing files."
             (push collection new-index)))))
     (setq org-persist--index (nreverse new-index))))
 
-;; Automatically write the data, but only when we have write access.
-(let ((dir (directory-file-name
-            (file-name-as-directory org-persist-directory))))
-  (while (and (not (file-exists-p dir))
-              (not (equal dir (setq dir (directory-file-name
-                                         (file-name-directory dir)))))))
-  (if (not (file-writable-p dir))
-      (message "Missing write access rights to org-persist-directory: %S"
-               org-persist-directory)
-    (add-hook 'kill-emacs-hook #'org-persist-write-all)
-    ;; `org-persist-gc' should run before `org-persist-write-all'.
-    ;; So we are adding the hook after `org-persist-write-all'.
-    (add-hook 'kill-emacs-hook #'org-persist-gc)))
+(defun org-persist-clear-storage-maybe ()
+  "Clear `org-persist-directory' according to `org-persist--disable-when-emacs-Q'.
+
+When `org-persist--disable-when-emacs-Q' is non-nil and Emacs is called with -Q
+command line argument, `org-persist-directory' is created in potentially public
+system temporary directory.  Remove everything upon existing Emacs in
+such scenario."
+  (when (and org-persist--disable-when-emacs-Q
+             ;; FIXME: This is relying on undocumented fact that
+             ;; Emacs sets `user-init-file' to nil when loaded with
+             ;; "-Q" argument.
+             (not user-init-file)
+             (file-exists-p org-persist-directory))
+    (delete-directory org-persist-directory 'recursive)))
 
 ;; Point to temp directory when `org-persist--disable-when-emacs-Q' is set.
 (when (and org-persist--disable-when-emacs-Q
@@ -984,11 +991,22 @@ Also, remove containers associated with non-existing files."
            ;; "-Q" argument.
            (not user-init-file))
   (setq org-persist-directory
-        (make-temp-file "org-persist-" 'dir))
-  ;; We don't need the temp directory to exist.
-  ;; `org-persist-write-all' will refrain from creating and writing to the dir if
-  ;; none exists yet.
-  (delete-directory org-persist-directory))
+        (make-temp-file "org-persist-" 'dir)))
+
+;; Automatically write the data, but only when we have write access.
+(let ((dir (directory-file-name
+            (file-name-as-directory org-persist-directory))))
+  (while (and (not (file-exists-p dir))
+              (not (equal dir (setq dir (directory-file-name
+                                       (file-name-directory dir)))))))
+  (if (not (file-writable-p dir))
+      (message "Missing write access rights to org-persist-directory: %S"
+               org-persist-directory)
+    (add-hook 'kill-emacs-hook #'org-persist-clear-storage-maybe) ; Run last.
+    (add-hook 'kill-emacs-hook #'org-persist-write-all)
+    ;; `org-persist-gc' should run before `org-persist-write-all'.
+    ;; So we are adding the hook after `org-persist-write-all'.
+    (add-hook 'kill-emacs-hook #'org-persist-gc)))
 
 (add-hook 'after-init-hook #'org-persist-load-all)