--- a/devtools/client/framework/toolbox-tabs-order-manager.js
+++ b/devtools/client/framework/toolbox-tabs-order-manager.js
@@ -20,16 +20,23 @@ class ToolboxTabsOrderManager {
     this.onMouseOut = this.onMouseOut.bind(this);
     this.onMouseUp = this.onMouseUp.bind(this);
 
     Services.prefs.addObserver(PREFERENCE_NAME, this.onOrderUpdated);
   }
 
   destroy() {
     Services.prefs.removeObserver(PREFERENCE_NAME, this.onOrderUpdated);
+
+    // Save the reordering preference, because some tools might be removed.
+    const ids =
+      this.currentPanelDefinitions.map(definition => definition.extensionId || definition.id);
+    const pref = ids.join(",");
+    Services.prefs.setCharPref(PREFERENCE_NAME, pref);
+
     this.onMouseUp();
   }
 
   setCurrentPanelDefinitions(currentPanelDefinitions) {
     this.currentPanelDefinitions = currentPanelDefinitions;
   }
 
   onMouseDown(e) {