diff --git a/code/lib/cli/package.json b/code/lib/cli/package.json
index e40de7032657..4ffce1dd476d 100644
--- a/code/lib/cli/package.json
+++ b/code/lib/cli/package.json
@@ -101,6 +101,7 @@
     "@types/semver": "^7.3.4",
     "@types/shelljs": "^0.8.7",
     "@types/util-deprecate": "^1.0.0",
+    "slash": "^5.0.0",
     "strip-json-comments": "^3.1.1",
     "typescript": "~4.9.3"
   },
diff --git a/code/lib/cli/src/automigrate/fixes/mdx-gfm.test.ts b/code/lib/cli/src/automigrate/fixes/mdx-gfm.test.ts
index b9143dd8f28d..55ec1971e7c3 100644
--- a/code/lib/cli/src/automigrate/fixes/mdx-gfm.test.ts
+++ b/code/lib/cli/src/automigrate/fixes/mdx-gfm.test.ts
@@ -3,6 +3,11 @@ import type { PackageJson } from '../../js-package-manager';
 import { makePackageManager, mockStorybookData } from '../helpers/testing-helpers';
 import { mdxgfm } from './mdx-gfm';
 
+jest.mock('globby', () => ({
+  __esModule: true,
+  default: jest.fn().mockResolvedValue(['a/fake/file.mdx']),
+}));
+
 const check = async ({
   packageJson,
   main: mainConfig,
@@ -88,7 +93,9 @@ describe('continue', () => {
     await expect(
       check({
         packageJson,
-        main: {},
+        main: {
+          stories: ['**/*.stories.mdx'],
+        },
       })
     ).resolves.toBeTruthy();
   });
@@ -97,6 +104,7 @@ describe('continue', () => {
       check({
         packageJson,
         main: {
+          stories: ['**/*.stories.mdx'],
           addons: [
             {
               name: '@storybook/addon-essentials',
@@ -118,6 +126,7 @@ describe('continue', () => {
       check({
         packageJson,
         main: {
+          stories: ['**/*.stories.mdx'],
           addons: ['@storybook/addon-essentials'],
         },
       })
diff --git a/code/lib/cli/src/automigrate/fixes/mdx-gfm.ts b/code/lib/cli/src/automigrate/fixes/mdx-gfm.ts
index 97e6b3f65e47..e4f0f6b8b7cd 100644
--- a/code/lib/cli/src/automigrate/fixes/mdx-gfm.ts
+++ b/code/lib/cli/src/automigrate/fixes/mdx-gfm.ts
@@ -1,5 +1,8 @@
 import { dedent } from 'ts-dedent';
 import semver from 'semver';
+import { join } from 'path';
+import slash from 'slash';
+import glob from 'globby';
 import { getStorybookData, updateMainConfig } from '../helpers/mainConfigFile';
 import type { Fix } from '../types';
 import { getStorybookVersionSpecifier } from '../../helpers';
@@ -22,9 +25,27 @@ export const mdxgfm: Fix<Options> = {
       return null;
     }
 
+    const hasMDXFiles = await mainConfig?.stories?.reduce(async (acc, item) => {
+      const val = await acc;
+
+      if (val === true) {
+        return true;
+      }
+
+      const pattern =
+        typeof item === 'string'
+          ? slash(join(configDir, item))
+          : slash(join(configDir, item.directory, item.files));
+
+      const files = await glob(pattern);
+
+      return files.some((f) => f.endsWith('.mdx'));
+    }, Promise.resolve(false));
+
     const usesMDX1 = mainConfig?.features?.legacyMdx1 === true || false;
     const skip =
       usesMDX1 ||
+      !hasMDXFiles ||
       !!mainConfig.addons?.find((item) => {
         if (item === '@storybook/addon-mdx-gfm') {
           return true;
diff --git a/code/yarn.lock b/code/yarn.lock
index 173a23b9ea72..1d668c8c55b4 100644
--- a/code/yarn.lock
+++ b/code/yarn.lock
@@ -5745,6 +5745,7 @@ __metadata:
     semver: ^7.3.7
     shelljs: ^0.8.5
     simple-update-notifier: ^1.0.0
+    slash: ^5.0.0
     strip-json-comments: ^3.1.1
     tempy: ^1.0.1
     ts-dedent: ^2.0.0