diff --git a/addons/a11y/src/a11yRunner.ts b/addons/a11y/src/a11yRunner.ts
index 5d60e10a67c8..c3f0b744f50d 100644
--- a/addons/a11y/src/a11yRunner.ts
+++ b/addons/a11y/src/a11yRunner.ts
@@ -2,21 +2,36 @@ import { document, window } from 'global';
 import axe from 'axe-core';
 import addons from '@storybook/addons';
 import { EVENTS } from './constants';
-import { Setup } from './params';
+import { A11yParameters } from './params';
 
 if (module && module.hot && module.hot.decline) {
   module.hot.decline();
 }
 
 const channel = addons.getChannel();
+// Holds axe core running state
 let active = false;
+// Holds latest story we requested a run
+let activeStoryId: string | undefined;
 
 const getElement = () => {
   const storyRoot = document.getElementById('story-root');
   return storyRoot ? storyRoot.children : document.getElementById('root');
 };
 
+/**
+ * Handle A11yContext events.
+ * Because the event are sent without manual check, we split calls
+ */
+const handleRequest = (storyId: string) => {
+  const { manual } = getParams(storyId);
+  if (!manual) {
+    run(storyId);
+  }
+};
+
 const run = async (storyId: string) => {
+  activeStoryId = storyId;
   try {
     const input = getParams(storyId);
 
@@ -24,14 +39,29 @@ const run = async (storyId: string) => {
       active = true;
       channel.emit(EVENTS.RUNNING);
 
-      const { element = getElement(), config, options } = input;
+      const {
+        element = getElement(),
+        config,
+        options = {
+          restoreScroll: true,
+        },
+      } = input;
       axe.reset();
       if (config) {
         axe.configure(config);
       }
 
       const result = await axe.run(element, options);
-      channel.emit(EVENTS.RESULT, result);
+      // It's possible that we requested a new run on a different story.
+      // Unfortunately, axe doesn't support a cancel method to abort current run.
+      // We check if the story we run against is still the current one,
+      // if not, trigger a new run using the current story
+      if (activeStoryId === storyId) {
+        channel.emit(EVENTS.RESULT, result);
+      } else {
+        active = false;
+        run(activeStoryId);
+      }
     }
   } catch (error) {
     channel.emit(EVENTS.ERROR, error);
@@ -41,7 +71,7 @@ const run = async (storyId: string) => {
 };
 
 /** Returns story parameters or default ones. */
-const getParams = (storyId: string): Setup => {
+const getParams = (storyId: string): A11yParameters => {
   const { parameters } = window.__STORYBOOK_STORY_STORE__.fromId(storyId) || {};
   return (
     parameters.a11y || {
@@ -53,5 +83,5 @@ const getParams = (storyId: string): Setup => {
   );
 };
 
-channel.on(EVENTS.REQUEST, run);
+channel.on(EVENTS.REQUEST, handleRequest);
 channel.on(EVENTS.MANUAL, run);
diff --git a/addons/a11y/src/components/A11YPanel.tsx b/addons/a11y/src/components/A11YPanel.tsx
index fc568cfc4e30..a00d6178440a 100644
--- a/addons/a11y/src/components/A11YPanel.tsx
+++ b/addons/a11y/src/components/A11YPanel.tsx
@@ -1,16 +1,16 @@
-import React, { useCallback, useMemo } from 'react';
+import React, { useCallback, useMemo, useState } from 'react';
 
 import { styled } from '@storybook/theming';
 
 import { ActionBar, Icons, ScrollArea } from '@storybook/components';
 
 import { AxeResults } from 'axe-core';
-import { useChannel, useParameter, useStorybookState, useAddonState } from '@storybook/api';
+import { useChannel, useParameter, useStorybookState } from '@storybook/api';
 import { Report } from './Report';
 import { Tabs } from './Tabs';
 
 import { useA11yContext } from './A11yContext';
-import { EVENTS, ADDON_ID } from '../constants';
+import { EVENTS } from '../constants';
 import { A11yParameters } from '../params';
 
 export enum RuleType {
@@ -51,13 +51,13 @@ const Centered = styled.span<{}>({
 type Status = 'initial' | 'manual' | 'running' | 'error' | 'ran' | 'ready';
 
 export const A11YPanel: React.FC = () => {
-  const [status, setStatus] = useAddonState<Status>(ADDON_ID, 'initial');
-  const [error, setError] = React.useState<unknown>(undefined);
-  const { setResults, results } = useA11yContext();
-  const { storyId } = useStorybookState();
   const { manual } = useParameter<Pick<A11yParameters, 'manual'>>('a11y', {
     manual: false,
   });
+  const [status, setStatus] = useState<Status>(manual ? 'manual' : 'initial');
+  const [error, setError] = React.useState<unknown>(undefined);
+  const { setResults, results } = useA11yContext();
+  const { storyId } = useStorybookState();
 
   React.useEffect(() => {
     setStatus(manual ? 'manual' : 'initial');
diff --git a/addons/a11y/src/components/A11yContext.tsx b/addons/a11y/src/components/A11yContext.tsx
index 458fa14f11b5..5061f5623d47 100644
--- a/addons/a11y/src/components/A11yContext.tsx
+++ b/addons/a11y/src/components/A11yContext.tsx
@@ -64,9 +64,9 @@ export const A11yContextProvider: React.FC<A11yContextProviderProps> = ({ active
         : prevHighlighted.filter((t) => !target.includes(t))
     );
   }, []);
-  const handleRun = React.useCallback(() => {
-    emit(EVENTS.REQUEST, storyId);
-  }, [storyId]);
+  const handleRun = (renderedStoryId: string) => {
+    emit(EVENTS.REQUEST, renderedStoryId);
+  };
   const handleClearHighlights = React.useCallback(() => setHighlighted([]), []);
   const handleSetTab = React.useCallback((index: number) => {
     handleClearHighlights();
@@ -90,7 +90,7 @@ export const A11yContextProvider: React.FC<A11yContextProviderProps> = ({ active
 
   React.useEffect(() => {
     if (active) {
-      handleRun();
+      handleRun(storyId);
     } else {
       handleClearHighlights();
     }
diff --git a/examples/official-storybook/stories/addon-a11y/typography.stories.js b/examples/official-storybook/stories/addon-a11y/typography.stories.js
index 8a8b12c4c575..1acf3b81bf23 100644
--- a/examples/official-storybook/stories/addon-a11y/typography.stories.js
+++ b/examples/official-storybook/stories/addon-a11y/typography.stories.js
@@ -34,3 +34,15 @@ EmptyLink.storyName = 'Empty Link';
 export const LinkWithoutHref = () => <a>{`${text}...`}</a>;
 
 LinkWithoutHref.storyName = 'Link without href';
+
+export const Manual = () => <p>I'm a manual run</p>;
+Manual.parameters = {
+  a11y: {
+    manual: true,
+    config: {
+      disableOtherRules: true,
+      rules: [],
+    },
+    options: {},
+  },
+};