diff --git a/x-pack/plugins/lens/public/app_plugin/app.tsx b/x-pack/plugins/lens/public/app_plugin/app.tsx
index 99f933361d40a..283d29e125683 100644
--- a/x-pack/plugins/lens/public/app_plugin/app.tsx
+++ b/x-pack/plugins/lens/public/app_plugin/app.tsx
@@ -10,8 +10,10 @@ import './app.scss';
 import React, { useState, useEffect, useCallback, useMemo } from 'react';
 import { i18n } from '@kbn/i18n';
 import { EuiBreadcrumb } from '@elastic/eui';
+import useLocalStorage from 'react-use/lib/useLocalStorage';
 import {
   createKbnUrlStateStorage,
+  Storage,
   withNotifyOnErrors,
 } from '../../../../../src/plugins/kibana_utils/public';
 import { useKibana } from '../../../../../src/plugins/kibana_react/public';
@@ -38,6 +40,7 @@ import { LensInspector } from '../lens_inspector_service';
 import { getEditPath } from '../../common';
 import { isLensEqual } from './lens_document_equality';
 import { disableAutoApply } from '../state_management/lens_slice';
+import { readFromStorage, writeToStorage } from '../settings_storage';
 
 export type SaveProps = Omit<OnSaveProps, 'onTitleDuplicate' | 'newDescription'> & {
   returnToOrigin: boolean;
@@ -296,10 +299,14 @@ export function App({
   );
 
   const autoApplyEnabled = !Boolean(appliedState);
-  const toggleAutoApply = useCallback(
-    () => dispatch(autoApplyEnabled ? disableAutoApply() : enableAutoApply()),
-    [dispatch, autoApplyEnabled]
-  );
+  const toggleAutoApply = useCallback(() => {
+    writeToStorage(
+      new Storage(localStorage),
+      'autoApplyDisabled',
+      String(typeof appliedState === 'undefined')
+    );
+    dispatch(autoApplyEnabled ? disableAutoApply() : enableAutoApply());
+  }, [dispatch, appliedState, autoApplyEnabled]);
 
   return (
     <>
diff --git a/x-pack/plugins/lens/public/settings_storage.tsx b/x-pack/plugins/lens/public/settings_storage.tsx
index fa59bff166c30..ebe812915242e 100644
--- a/x-pack/plugins/lens/public/settings_storage.tsx
+++ b/x-pack/plugins/lens/public/settings_storage.tsx
@@ -14,5 +14,5 @@ export const readFromStorage = (storage: IStorageWrapper, key: string) => {
   return data && data[key];
 };
 export const writeToStorage = (storage: IStorageWrapper, key: string, value: string) => {
-  storage.set(STORAGE_KEY, { [key]: value });
+  storage.set(STORAGE_KEY, { ...storage.get(STORAGE_KEY), [key]: value });
 };
diff --git a/x-pack/plugins/lens/public/state_management/init_middleware/load_initial.ts b/x-pack/plugins/lens/public/state_management/init_middleware/load_initial.ts
index 372d08017ee2a..f649fef25d718 100644
--- a/x-pack/plugins/lens/public/state_management/init_middleware/load_initial.ts
+++ b/x-pack/plugins/lens/public/state_management/init_middleware/load_initial.ts
@@ -9,7 +9,7 @@ import { MiddlewareAPI } from '@reduxjs/toolkit';
 import { i18n } from '@kbn/i18n';
 import { History } from 'history';
 import { setState, initEmpty, LensStoreDeps } from '..';
-import { getPreloadedState } from '../lens_slice';
+import { disableAutoApply, getPreloadedState } from '../lens_slice';
 import { SharingSavedObjectProps } from '../../types';
 import { LensEmbeddableInput, LensByReferenceInput } from '../../embeddable/embeddable';
 import { getInitialDatasourceId } from '../../utils';
@@ -17,6 +17,8 @@ import { initializeDatasources } from '../../editor_frame_service/editor_frame';
 import { LensAppServices } from '../../app_plugin/types';
 import { getEditPath, getFullPath, LENS_EMBEDDABLE_TYPE } from '../../../common/constants';
 import { Document } from '../../persistence';
+import { readFromStorage } from '../../settings_storage';
+import { Storage } from '../../../../../../src/plugins/kibana_utils/public';
 
 export const getPersisted = async ({
   initialInput,
@@ -209,6 +211,12 @@ export function loadInitial(
                   isLoading: false,
                 })
               );
+
+              const autoApplyDisabled =
+                readFromStorage(new Storage(localStorage), 'autoApplyDisabled') === 'true';
+              if (autoApplyDisabled) {
+                store.dispatch(disableAutoApply());
+              }
             })
             .catch((e: { message: string }) =>
               notifications.toasts.addDanger({