diff --git a/gnucash/gnome-utils/gnc-main-window.c b/gnucash/gnome-utils/gnc-main-window.c
index 312d121318..5892130e67 100644
--- a/gnucash/gnome-utils/gnc-main-window.c
+++ b/gnucash/gnome-utils/gnc-main-window.c
@@ -1146,6 +1146,11 @@ gnc_main_window_all_finish_pending (void)
             return FALSE;
         }
     }
+    if (gnc_gui_refresh_suspended ())
+    {
+        gnc_warning_dialog (NULL, "%s", "An operation is still pending, wait for it to complete before quitting ");
+        return FALSE;
+    }
     return TRUE;
 }
 
@@ -3707,7 +3712,7 @@ static gboolean
 gnc_quartz_should_quit (GtkosxApplication *theApp, GncMainWindow *window)
 {
     if (gnc_main_window_all_finish_pending())
-        return gnc_main_window_quit (window);
+        return !gnc_main_window_quit (window);
     return TRUE;
 }
 
diff --git a/gnucash/gnome/gnc-plugin-page-account-tree.c b/gnucash/gnome/gnc-plugin-page-account-tree.c
index f664066025..1c7554bf22 100644
--- a/gnucash/gnome/gnc-plugin-page-account-tree.c
+++ b/gnucash/gnome/gnc-plugin-page-account-tree.c
@@ -413,6 +413,30 @@ gnc_plugin_page_account_tree_new (void)
 
 G_DEFINE_TYPE_WITH_PRIVATE(GncPluginPageAccountTree, gnc_plugin_page_account_tree, GNC_TYPE_PLUGIN_PAGE)
 
+static void
+prepare_scrubbing ()
+{
+    gnc_suspend_gui_refresh ();
+    gnc_set_abort_scrub (FALSE);
+}
+
+static gboolean
+finish (GncPluginPage* page)
+{
+    if (gnc_get_ongoing_scrub ())
+    {
+        gboolean ret = gnc_verify_dialog (NULL, FALSE, "%s", "A scrubbing operation is currently pending, do you want to abort it?");
+        if (ret)
+        {
+            gnc_set_abort_scrub (TRUE);
+            gnc_resume_gui_refresh (); // This is so quit does not complain about an ongoing operation.
+            return TRUE;
+        }
+        return FALSE;
+    }
+    return TRUE;
+}
+
 static void
 gnc_plugin_page_account_tree_class_init (GncPluginPageAccountTreeClass *klass)
 {
@@ -430,6 +454,8 @@ gnc_plugin_page_account_tree_class_init (GncPluginPageAccountTreeClass *klass)
     gnc_plugin_class->save_page       = gnc_plugin_page_account_tree_save_page;
     gnc_plugin_class->recreate_page   = gnc_plugin_page_account_tree_recreate_page;
     gnc_plugin_class->focus_page_function = gnc_plugin_page_account_tree_focus_widget;
+    gnc_plugin_class->finish_pending = finish;
+
 
     plugin_page_signals[ACCOUNT_SELECTED] =
         g_signal_new ("account_selected",
@@ -1913,7 +1939,7 @@ gnc_plugin_page_account_tree_cmd_scrub (GtkAction *action, GncPluginPageAccountT
 
     g_return_if_fail (account != NULL);
 
-    gnc_suspend_gui_refresh ();
+    prepare_scrubbing ();
 
     window = GNC_WINDOW(GNC_PLUGIN_PAGE (page)->window);
     gnc_window_set_progressbar_window (window);
@@ -1939,7 +1965,7 @@ gnc_plugin_page_account_tree_cmd_scrub_sub (GtkAction *action, GncPluginPageAcco
 
     g_return_if_fail (account != NULL);
 
-    gnc_suspend_gui_refresh ();
+    prepare_scrubbing ();
 
     window = GNC_WINDOW(GNC_PLUGIN_PAGE (page)->window);
     gnc_window_set_progressbar_window (window);
@@ -1962,7 +1988,7 @@ gnc_plugin_page_account_tree_cmd_scrub_all (GtkAction *action, GncPluginPageAcco
     Account *root = gnc_get_current_root_account ();
     GncWindow *window;
 
-    gnc_suspend_gui_refresh ();
+    prepare_scrubbing ();
 
     window = GNC_WINDOW(GNC_PLUGIN_PAGE (page)->window);
     gnc_window_set_progressbar_window (window);
diff --git a/gnucash/gnome/gnc-plugin-page-register.c b/gnucash/gnome/gnc-plugin-page-register.c
index 4bb4d44e05..235bf13235 100644
--- a/gnucash/gnome/gnc-plugin-page-register.c
+++ b/gnucash/gnome/gnc-plugin-page-register.c
@@ -1912,6 +1912,25 @@ gnc_plugin_page_register_update_edit_menu (GncPluginPage* page, gboolean hide)
     gtk_action_set_visible (action,  !hide || can_paste);
 }
 
+static gboolean abort_scrub = FALSE;
+static gboolean is_scrubbing = FALSE;
+
+static gboolean
+finish_scrub (GncPluginPage* page)
+{
+    if (is_scrubbing)
+    {
+        gboolean ret = gnc_verify_dialog (NULL, FALSE, "%s", "A scrubbing operation is currently pending, do you want to abort it?");
+        if (ret)
+        {
+            abort_scrub = TRUE;
+            gnc_resume_gui_refresh (); // This is so quit does not complain about an ongoing operation.
+            return TRUE;
+        }
+        return FALSE;
+    }
+    return TRUE;
+}
 
 static gboolean
 gnc_plugin_page_register_finish_pending (GncPluginPage* page)
@@ -1923,6 +1942,9 @@ gnc_plugin_page_register_finish_pending (GncPluginPage* page)
     const gchar* name;
     gint response;
 
+    if (!finish_scrub (page))
+        return FALSE;
+    
     reg_page = GNC_PLUGIN_PAGE_REGISTER (page);
     priv = GNC_PLUGIN_PAGE_REGISTER_GET_PRIVATE (reg_page);
     reg = gnc_ledger_display_get_split_register (priv->ledger);
@@ -4977,6 +4999,7 @@ gnc_plugin_page_register_cmd_scrub_all (GtkAction* action,
     }
 
     gnc_suspend_gui_refresh();
+    is_scrubbing = TRUE;
     window = GNC_WINDOW (GNC_PLUGIN_PAGE (plugin_page)->window);
     gnc_window_set_progressbar_window (window);
 
@@ -5000,6 +5023,8 @@ gnc_plugin_page_register_cmd_scrub_all (GtkAction* action,
             char* progress_msg = g_strdup_printf (message, curr_split_no, split_count);
             gnc_window_show_progress (progress_msg, (100 * curr_split_no) / split_count);
             g_free (progress_msg);
+            if (abort_scrub)
+                break;
         }
 
         xaccTransScrubOrphans (trans);
@@ -5020,6 +5045,7 @@ gnc_plugin_page_register_cmd_scrub_all (GtkAction* action,
 
     gnc_window_show_progress (NULL, -1.0);
     gnc_resume_gui_refresh();
+    is_scrubbing = FALSE;
     LEAVE (" ");
 }
 
diff --git a/libgnucash/engine/Scrub.c b/libgnucash/engine/Scrub.c
index 63ab6d90ab..9efb9e93c7 100644
--- a/libgnucash/engine/Scrub.c
+++ b/libgnucash/engine/Scrub.c
@@ -57,6 +57,20 @@
 #define G_LOG_DOMAIN "gnc.engine.scrub"
 
 static QofLogModule log_module = G_LOG_DOMAIN;
+static gboolean abort_now = FALSE;
+static gint scrub_depth = 0;
+
+void
+gnc_set_abort_scrub (gboolean abort)
+{
+    abort_now = abort;
+}
+
+gboolean
+gnc_get_ongoing_scrub (void)
+{
+    return scrub_depth > 0;
+}
 
 /* ================================================================ */
 
@@ -64,10 +78,11 @@ void
 xaccAccountTreeScrubOrphans (Account *acc, QofPercentageFunc percentagefunc)
 {
     if (!acc) return;
-
+    scrub_depth ++;
     xaccAccountScrubOrphans (acc, percentagefunc);
     gnc_account_foreach_descendant(acc,
                                    (AccountCb)xaccAccountScrubOrphans, percentagefunc);
+    scrub_depth--;
 }
 
 static void
@@ -83,6 +98,7 @@ TransScrubOrphansFast (Transaction *trans, Account *root)
     {
         Split *split = node->data;
         Account *orph;
+        if (abort_now) break;
 
         if (split->acc) continue;
 
@@ -110,6 +126,7 @@ xaccAccountScrubOrphans (Account *acc, QofPercentageFunc percentagefunc)
     guint current_split = 0;
 
     if (!acc) return;
+    scrub_depth++;
 
     str = xaccAccountGetName (acc);
     str = str ? str : "(null)";
@@ -120,12 +137,12 @@ xaccAccountScrubOrphans (Account *acc, QofPercentageFunc percentagefunc)
     for (node = splits; node; node = node->next)
     {
         Split *split = node->data;
-
         if (current_split % 100 == 0)
         {
             char *progress_msg = g_strdup_printf (message, str, current_split, total_splits);
             (percentagefunc)(progress_msg, (100 * current_split) / total_splits);
             g_free (progress_msg);
+            if (abort_now) break;
         }
 
         TransScrubOrphansFast (xaccSplitGetParent (split),
@@ -133,6 +150,7 @@ xaccAccountScrubOrphans (Account *acc, QofPercentageFunc percentagefunc)
         current_split++;
     }
     (percentagefunc)(NULL, -1.0);
+    scrub_depth--;
 }
 
 
@@ -148,6 +166,7 @@ xaccTransScrubOrphans (Transaction *trans)
     for (node = trans->splits; node; node = node->next)
     {
         Split *split = node->data;
+        if (abort_now) break;
 
         if (split->acc)
         {
@@ -183,9 +202,13 @@ void
 xaccAccountScrubSplits (Account *account)
 {
     GList *node;
-
+    scrub_depth++;
     for (node = xaccAccountGetSplitList (account); node; node = node->next)
+    {
+        if (abort_now) break;
         xaccSplitScrub (node->data);
+    }
+    scrub_depth--;
 }
 
 void
@@ -291,9 +314,11 @@ xaccSplitScrub (Split *split)
 void
 xaccAccountTreeScrubImbalance (Account *acc, QofPercentageFunc percentagefunc)
 {
+    scrub_depth++;
     xaccAccountScrubImbalance (acc, percentagefunc);
     gnc_account_foreach_descendant(acc,
                                    (AccountCb)xaccAccountScrubImbalance, percentagefunc);
+    scrub_depth--;
 }
 
 void
@@ -305,6 +330,7 @@ xaccAccountScrubImbalance (Account *acc, QofPercentageFunc percentagefunc)
     gint split_count = 0, curr_split_no = 0;
 
     if (!acc) return;
+    scrub_depth++;
 
     str = xaccAccountGetName(acc);
     str = str ? str : "(null)";
@@ -316,6 +342,7 @@ xaccAccountScrubImbalance (Account *acc, QofPercentageFunc percentagefunc)
     {
         Split *split = node->data;
         Transaction *trans = xaccSplitGetParent(split);
+        if (abort_now) break;
 
         PINFO("Start processing split %d of %d",
               curr_split_no + 1, split_count);
@@ -340,6 +367,7 @@ xaccAccountScrubImbalance (Account *acc, QofPercentageFunc percentagefunc)
         curr_split_no++;
     }
     (percentagefunc)(NULL, -1.0);
+    scrub_depth--;
 }
 
 static Split *
@@ -1243,19 +1271,22 @@ scrub_trans_currency_helper (Transaction *t, gpointer data)
 static void
 scrub_account_commodity_helper (Account *account, gpointer data)
 {
+    scrub_depth++;
     xaccAccountScrubCommodity (account);
     xaccAccountDeleteOldData (account);
+    scrub_depth--;
 }
 
 void
 xaccAccountTreeScrubCommodities (Account *acc)
 {
     if (!acc) return;
-
+    scrub_depth++;
     xaccAccountTreeForEachTransaction (acc, scrub_trans_currency_helper, NULL);
 
     scrub_account_commodity_helper (acc, NULL);
     gnc_account_foreach_descendant (acc, scrub_account_commodity_helper, NULL);
+    scrub_depth--;
 }
 
 /* ================================================================ */
@@ -1315,13 +1346,14 @@ xaccAccountTreeScrubQuoteSources (Account *root, gnc_commodity_table *table)
         LEAVE("Oops");
         return;
     }
-
+    scrub_depth++;
     gnc_commodity_table_foreach_commodity (table, check_quote_source, &new_style);
 
     move_quote_source(root, GINT_TO_POINTER(new_style));
     gnc_account_foreach_descendant (root, move_quote_source,
                                     GINT_TO_POINTER(new_style));
     LEAVE("Migration done");
+    scrub_depth--;
 }
 
 /* ================================================================ */
@@ -1333,6 +1365,7 @@ xaccAccountScrubKvp (Account *account)
     gchar *str2;
 
     if (!account) return;
+    scrub_depth++;
 
     qof_instance_get_kvp (QOF_INSTANCE (account), &v, 1, "notes");
     if (G_VALUE_HOLDS_STRING (&v))
@@ -1350,6 +1383,7 @@ xaccAccountScrubKvp (Account *account)
         qof_instance_slot_delete (QOF_INSTANCE (account), "placeholder");
 
     qof_instance_slot_delete_if_empty (QOF_INSTANCE (account), "hbci");
+    scrub_depth--;
 }
 
 /* ================================================================ */
diff --git a/libgnucash/engine/Scrub.h b/libgnucash/engine/Scrub.h
index 9536f8c34b..bfaea845af 100644
--- a/libgnucash/engine/Scrub.h
+++ b/libgnucash/engine/Scrub.h
@@ -69,6 +69,16 @@
     for orphaned inodes.
     @{  */
 
+/** The gnc_set_abort_scrub () method causes a currently running scrub operation
+ *    to stop, if abort is TRUE; gnc_set_abort_scrub(FALSE) must be called before
+ *    any scrubbing operation.
+ */
+void gnc_set_abort_scrub (gboolean abort);
+
+/** The gnc_get_ongoing_scrub () method returns TRUE if a scrub operation is ongoing.
+ */
+gboolean gnc_get_ongoing_scrub (void);
+
 /** The xaccTransScrubOrphans() method scrubs only the splits in the
  *    given transaction.
  */