diff --git a/.changeset/calm-bottles-rest.md b/.changeset/calm-bottles-rest.md
new file mode 100644
index 0000000000..56321279e0
--- /dev/null
+++ b/.changeset/calm-bottles-rest.md
@@ -0,0 +1,5 @@
+---
+'@backstage/cli': patch
+---
+
+Internal change to move the `migrate` and `version:*` commands into a new migrate module.
diff --git a/packages/cli/cli-report.md b/packages/cli/cli-report.md
index 7673a2e905..02051b69f7 100644
--- a/packages/cli/cli-report.md
+++ b/packages/cli/cli-report.md
@@ -19,10 +19,10 @@ Commands:
   config:schema [options]
   repo [command]
   package [command]
-  migrate [command]
-  build-workspace [options] <workspace-dir> [packages...]
   versions:bump [options]
   versions:migrate [options]
+  migrate [command]
+  build-workspace [options] <workspace-dir> [packages...]
   create-github-app <github-org>
   info
   help [command]
diff --git a/packages/cli/src/alpha.ts b/packages/cli/src/alpha.ts
index 8f197767bb..85a8763974 100644
--- a/packages/cli/src/alpha.ts
+++ b/packages/cli/src/alpha.ts
@@ -26,5 +26,6 @@ import chalk from 'chalk';
   const initializer = new CliInitializer();
   initializer.add(import('./modules/config/alpha'));
   initializer.add(import('./modules/build/alpha'));
+  initializer.add(import('./modules/migrate/alpha'));
   await initializer.run();
 })();
diff --git a/packages/cli/src/commands/index.ts b/packages/cli/src/commands/index.ts
index 31bf4ef669..ee2af9541c 100644
--- a/packages/cli/src/commands/index.ts
+++ b/packages/cli/src/commands/index.ts
@@ -25,6 +25,7 @@ import {
   registerRepoCommands as registerRepoBuildCommands,
   registerCommands as registerBuildCommands,
 } from '../modules/build';
+import { registerCommands as registerMigrateCommand } from '../modules/migrate';
 
 export function registerRepoCommand(program: Command) {
   const command = program
@@ -171,41 +172,6 @@ export function registerScriptCommand(program: Command) {
     .action(lazy(() => import('./pack'), 'post'));
 }
 
-export function registerMigrateCommand(program: Command) {
-  const command = program
-    .command('migrate [command]')
-    .description('Migration utilities');
-
-  command
-    .command('package-roles')
-    .description(`Add package role field to packages that don't have it`)
-    .action(lazy(() => import('./migrate/packageRole'), 'default'));
-
-  command
-    .command('package-scripts')
-    .description('Set package scripts according to each package role')
-    .action(lazy(() => import('./migrate/packageScripts'), 'command'));
-
-  command
-    .command('package-exports')
-    .description('Synchronize package subpath export definitions')
-    .action(lazy(() => import('./migrate/packageExports'), 'command'));
-
-  command
-    .command('package-lint-configs')
-    .description(
-      'Migrates all packages to use @backstage/cli/config/eslint-factory',
-    )
-    .action(lazy(() => import('./migrate/packageLintConfigs'), 'command'));
-
-  command
-    .command('react-router-deps')
-    .description(
-      'Migrates the react-router dependencies for all packages to be peer dependencies',
-    )
-    .action(lazy(() => import('./migrate/reactRouterDeps'), 'command'));
-}
-
 export function registerCommands(program: Command) {
   program
     .command('new')
@@ -249,37 +215,6 @@ export function registerCommands(program: Command) {
   registerMigrateCommand(program);
   registerBuildCommands(program);
 
-  program
-    .command('versions:bump')
-    .option(
-      '--pattern <glob>',
-      'Override glob for matching packages to upgrade',
-    )
-    .option(
-      '--release <version|next|main>',
-      'Bump to a specific Backstage release line or version',
-      'main',
-    )
-    .option('--skip-install', 'Skips yarn install step')
-    .option('--skip-migrate', 'Skips migration of any moved packages')
-    .description('Bump Backstage packages to the latest versions')
-    .action(lazy(() => import('./versions/bump'), 'default'));
-
-  program
-    .command('versions:migrate')
-    .option(
-      '--pattern <glob>',
-      'Override glob for matching packages to upgrade',
-    )
-    .option(
-      '--skip-code-changes',
-      'Skip code changes and only update package.json files',
-    )
-    .description(
-      'Migrate any plugins that have been moved to the @backstage-community namespace automatically',
-    )
-    .action(lazy(() => import('./versions/migrate'), 'default'));
-
   program
     .command('create-github-app <github-org>')
     .description('Create new GitHub App in your organization.')
diff --git a/packages/cli/src/modules/migrate/alpha.ts b/packages/cli/src/modules/migrate/alpha.ts
new file mode 100644
index 0000000000..ac56c06b7a
--- /dev/null
+++ b/packages/cli/src/modules/migrate/alpha.ts
@@ -0,0 +1,135 @@
+/*
+ * Copyright 2024 The Backstage Authors
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+import { createCliPlugin } from '../../wiring/factory';
+import { Command } from 'commander';
+import { lazy } from '../../lib/lazy';
+
+export default createCliPlugin({
+  pluginId: 'migrate',
+  init: async reg => {
+    reg.addCommand({
+      path: ['versions:migrate'],
+      description:
+        'Migrate any plugins that have been moved to the @backstage-community namespace automatically',
+      execute: async ({ args }) => {
+        const command = new Command();
+        const defaultCommand = command
+          .option(
+            '--pattern <glob>',
+            'Override glob for matching packages to upgrade',
+          )
+          .option(
+            '--skip-code-changes',
+            'Skip code changes and only update package.json files',
+          )
+          .action(lazy(() => import('./commands/versions/migrate'), 'default'));
+
+        await defaultCommand.parseAsync(args, { from: 'user' });
+      },
+    });
+
+    reg.addCommand({
+      path: ['versions:bump'],
+      description: 'Bump Backstage packages to the latest versions',
+      execute: async ({ args }) => {
+        const command = new Command();
+
+        const defaultCommand = command
+          .option(
+            '--pattern <glob>',
+            'Override glob for matching packages to upgrade',
+          )
+          .option(
+            '--release <version|next|main>',
+            'Bump to a specific Backstage release line or version',
+            'main',
+          )
+          .option('--skip-install', 'Skips yarn install step')
+          .option('--skip-migrate', 'Skips migration of any moved packages')
+          .action(lazy(() => import('./commands/versions/bump'), 'default'));
+
+        await defaultCommand.parseAsync(args, { from: 'user' });
+      },
+    });
+
+    reg.addCommand({
+      path: ['migrate', 'package-roles'],
+      description: `Add package role field to packages that don't have it`,
+      execute: async ({ args }) => {
+        const command = new Command();
+        const defaultCommand = command.action(
+          lazy(() => import('./commands/packageRole'), 'default'),
+        );
+
+        await defaultCommand.parseAsync(args, { from: 'user' });
+      },
+    });
+
+    reg.addCommand({
+      path: ['migrate', 'package-scripts'],
+      description: 'Set package scripts according to each package role',
+      execute: async ({ args }) => {
+        const command = new Command();
+        const defaultCommand = command.action(
+          lazy(() => import('./commands/packageScripts'), 'command'),
+        );
+
+        await defaultCommand.parseAsync(args, { from: 'user' });
+      },
+    });
+
+    reg.addCommand({
+      path: ['migrate', 'package-exports'],
+      description: 'Synchronize package subpath export definitions',
+      execute: async ({ args }) => {
+        const command = new Command();
+        const defaultCommand = command.action(
+          lazy(() => import('./commands/packageExports'), 'command'),
+        );
+
+        await defaultCommand.parseAsync(args, { from: 'user' });
+      },
+    });
+
+    reg.addCommand({
+      path: ['migrate', 'package-lint-configs'],
+      description:
+        'Migrates all packages to use @backstage/cli/config/eslint-factory',
+      execute: async ({ args }) => {
+        const command = new Command();
+        const defaultCommand = command.action(
+          lazy(() => import('./commands/packageLintConfigs'), 'command'),
+        );
+
+        await defaultCommand.parseAsync(args, { from: 'user' });
+      },
+    });
+
+    reg.addCommand({
+      path: ['migrate', 'react-router-deps'],
+      description:
+        'Migrates the react-router dependencies for all packages to be peer dependencies',
+      execute: async ({ args }) => {
+        const command = new Command();
+        const defaultCommand = command.action(
+          lazy(() => import('./commands/reactRouterDeps'), 'command'),
+        );
+
+        await defaultCommand.parseAsync(args, { from: 'user' });
+      },
+    });
+  },
+});
diff --git a/packages/cli/src/commands/migrate/packageExports.ts b/packages/cli/src/modules/migrate/commands/packageExports.ts
similarity index 96%
rename from packages/cli/src/commands/migrate/packageExports.ts
rename to packages/cli/src/modules/migrate/commands/packageExports.ts
index 6757d01bbe..c54422ceb9 100644
--- a/packages/cli/src/commands/migrate/packageExports.ts
+++ b/packages/cli/src/modules/migrate/commands/packageExports.ts
@@ -18,7 +18,7 @@ import {
   fixPackageExports,
   readFixablePackages,
   writeFixedPackages,
-} from '../repo/fix';
+} from '../../../commands/repo/fix';
 
 export async function command() {
   console.log(
diff --git a/packages/cli/src/commands/migrate/packageLintConfigs.ts b/packages/cli/src/modules/migrate/commands/packageLintConfigs.ts
similarity index 98%
rename from packages/cli/src/commands/migrate/packageLintConfigs.ts
rename to packages/cli/src/modules/migrate/commands/packageLintConfigs.ts
index 03d42846e8..c8e8ef3a42 100644
--- a/packages/cli/src/commands/migrate/packageLintConfigs.ts
+++ b/packages/cli/src/modules/migrate/commands/packageLintConfigs.ts
@@ -17,7 +17,7 @@
 import fs from 'fs-extra';
 import { resolve as resolvePath } from 'path';
 import { PackageGraph } from '@backstage/cli-node';
-import { runPlain } from '../../lib/run';
+import { runPlain } from '../../../lib/run';
 
 const PREFIX = `module.exports = require('@backstage/cli/config/eslint-factory')`;
 
diff --git a/packages/cli/src/commands/migrate/packageRole.ts b/packages/cli/src/modules/migrate/commands/packageRole.ts
similarity index 98%
rename from packages/cli/src/commands/migrate/packageRole.ts
rename to packages/cli/src/modules/migrate/commands/packageRole.ts
index e7abbd3dcd..9a4bb08f6a 100644
--- a/packages/cli/src/commands/migrate/packageRole.ts
+++ b/packages/cli/src/modules/migrate/commands/packageRole.ts
@@ -18,7 +18,7 @@ import fs from 'fs-extra';
 import { resolve as resolvePath } from 'path';
 import { getPackages } from '@manypkg/get-packages';
 import { PackageRoles } from '@backstage/cli-node';
-import { paths } from '../../lib/paths';
+import { paths } from '../../../lib/paths';
 
 export default async () => {
   const { packages } = await getPackages(paths.targetDir);
diff --git a/packages/cli/src/commands/migrate/packageScripts.ts b/packages/cli/src/modules/migrate/commands/packageScripts.ts
similarity index 100%
rename from packages/cli/src/commands/migrate/packageScripts.ts
rename to packages/cli/src/modules/migrate/commands/packageScripts.ts
diff --git a/packages/cli/src/commands/migrate/reactRouterDeps.ts b/packages/cli/src/modules/migrate/commands/reactRouterDeps.ts
similarity index 100%
rename from packages/cli/src/commands/migrate/reactRouterDeps.ts
rename to packages/cli/src/modules/migrate/commands/reactRouterDeps.ts
diff --git a/packages/cli/src/commands/versions/bump.test.ts b/packages/cli/src/modules/migrate/commands/versions/bump.test.ts
similarity index 99%
rename from packages/cli/src/commands/versions/bump.test.ts
rename to packages/cli/src/modules/migrate/commands/versions/bump.test.ts
index d3ff0c1fbe..bce9888842 100644
--- a/packages/cli/src/commands/versions/bump.test.ts
+++ b/packages/cli/src/modules/migrate/commands/versions/bump.test.ts
@@ -16,10 +16,10 @@
 
 import fs from 'fs-extra';
 import { Command } from 'commander';
-import * as runObj from '../../lib/run';
+import * as runObj from '../../../../lib/run';
 import bump, { bumpBackstageJsonVersion, createVersionFinder } from './bump';
 import { registerMswTestHooks, withLogCollector } from '@backstage/test-utils';
-import { YarnInfoInspectData } from '../../lib/versioning/packages';
+import { YarnInfoInspectData } from '../../../../lib/versioning/packages';
 import { setupServer } from 'msw/node';
 import { rest } from 'msw';
 import { NotFoundError } from '@backstage/errors';
@@ -73,15 +73,15 @@ jest.mock('@backstage/cli-common', () => ({
   }),
 }));
 
-jest.mock('../../lib/run', () => {
+jest.mock('../../../../lib/run', () => {
   return {
     run: jest.fn(),
   };
 });
 
 const mockFetchPackageInfo = jest.fn();
-jest.mock('../../lib/versioning/packages', () => {
-  const actual = jest.requireActual('../../lib/versioning/packages');
+jest.mock('../../../../lib/versioning/packages', () => {
+  const actual = jest.requireActual('../../../../lib/versioning/packages');
   return {
     ...actual,
     fetchPackageInfo: (name: string) => mockFetchPackageInfo(name),
diff --git a/packages/cli/src/commands/versions/bump.ts b/packages/cli/src/modules/migrate/commands/versions/bump.ts
similarity index 98%
rename from packages/cli/src/commands/versions/bump.ts
rename to packages/cli/src/modules/migrate/commands/versions/bump.ts
index 6f8ce0a8a0..23202ee1b5 100644
--- a/packages/cli/src/commands/versions/bump.ts
+++ b/packages/cli/src/modules/migrate/commands/versions/bump.ts
@@ -24,23 +24,23 @@ import yaml from 'yaml';
 import z from 'zod';
 import { isError, NotFoundError } from '@backstage/errors';
 import { resolve as resolvePath } from 'path';
-import { paths } from '../../lib/paths';
+import { paths } from '../../../../lib/paths';
 import {
   mapDependencies,
   fetchPackageInfo,
   Lockfile,
   YarnInfoInspectData,
-} from '../../lib/versioning';
+} from '../../../../lib/versioning';
 import { BACKSTAGE_JSON } from '@backstage/cli-common';
-import { runParallelWorkers } from '../../lib/parallel';
+import { runParallelWorkers } from '../../../../lib/parallel';
 import {
   getManifestByReleaseLine,
   getManifestByVersion,
   ReleaseManifest,
 } from '@backstage/release-manifests';
 import { migrateMovedPackages } from './migrate';
-import { runYarnInstall } from './utils';
-import { run } from '../../lib/run';
+import { runYarnInstall } from '../../lib/utils';
+import { run } from '../../../../lib/run';
 
 function maybeBootstrapProxy() {
   // see https://www.npmjs.com/package/global-agent
diff --git a/packages/cli/src/commands/versions/migrate.test.ts b/packages/cli/src/modules/migrate/commands/versions/migrate.test.ts
similarity index 99%
rename from packages/cli/src/commands/versions/migrate.test.ts
rename to packages/cli/src/modules/migrate/commands/versions/migrate.test.ts
index 919eb18278..7a0a1269c4 100644
--- a/packages/cli/src/commands/versions/migrate.test.ts
+++ b/packages/cli/src/modules/migrate/commands/versions/migrate.test.ts
@@ -17,7 +17,7 @@ import {
   MockDirectory,
   createMockDirectory,
 } from '@backstage/backend-test-utils';
-import * as run from '../../lib/run';
+import * as run from '../../../../lib/run';
 import migrate from './migrate';
 import { withLogCollector } from '@backstage/test-utils';
 import fs from 'fs-extra';
@@ -45,7 +45,7 @@ jest.mock('@backstage/cli-common', () => ({
   }),
 }));
 
-jest.mock('../../lib/run', () => {
+jest.mock('../../../../lib/run', () => {
   return {
     run: jest.fn(),
   };
diff --git a/packages/cli/src/commands/versions/migrate.ts b/packages/cli/src/modules/migrate/commands/versions/migrate.ts
similarity index 98%
rename from packages/cli/src/commands/versions/migrate.ts
rename to packages/cli/src/modules/migrate/commands/versions/migrate.ts
index 8415de0f57..7825ea31cb 100644
--- a/packages/cli/src/commands/versions/migrate.ts
+++ b/packages/cli/src/modules/migrate/commands/versions/migrate.ts
@@ -19,7 +19,7 @@ import { resolve as resolvePath, join as joinPath } from 'path';
 import { OptionValues } from 'commander';
 import { readJson, writeJson } from 'fs-extra';
 import { minimatch } from 'minimatch';
-import { runYarnInstall } from './utils';
+import { runYarnInstall } from '../../lib/utils';
 import replace from 'replace-in-file';
 
 declare module 'replace-in-file' {
diff --git a/packages/cli/src/modules/migrate/index.ts b/packages/cli/src/modules/migrate/index.ts
new file mode 100644
index 0000000000..10e96ad173
--- /dev/null
+++ b/packages/cli/src/modules/migrate/index.ts
@@ -0,0 +1,84 @@
+/*
+ * Copyright 2025 The Backstage Authors
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+import { lazy } from '../../lib/lazy';
+import { Command } from 'commander';
+
+export function registerCommands(program: Command) {
+  program
+    .command('versions:bump')
+    .option(
+      '--pattern <glob>',
+      'Override glob for matching packages to upgrade',
+    )
+    .option(
+      '--release <version|next|main>',
+      'Bump to a specific Backstage release line or version',
+      'main',
+    )
+    .option('--skip-install', 'Skips yarn install step')
+    .option('--skip-migrate', 'Skips migration of any moved packages')
+    .description('Bump Backstage packages to the latest versions')
+    .action(lazy(() => import('./commands/versions/bump'), 'default'));
+
+  program
+    .command('versions:migrate')
+    .option(
+      '--pattern <glob>',
+      'Override glob for matching packages to upgrade',
+    )
+    .option(
+      '--skip-code-changes',
+      'Skip code changes and only update package.json files',
+    )
+    .description(
+      'Migrate any plugins that have been moved to the @backstage-community namespace automatically',
+    )
+    .action(lazy(() => import('./commands/versions/migrate'), 'default'));
+
+  const command = program
+    .command('migrate [command]')
+    .description('Migration utilities');
+
+  command
+    .command('package-roles')
+    .description(`Add package role field to packages that don't have it`)
+    .action(lazy(() => import('./commands/packageRole'), 'default'));
+
+  command
+    .command('package-scripts')
+    .description('Set package scripts according to each package role')
+    .action(lazy(() => import('./commands/packageScripts'), 'command'));
+
+  command
+    .command('package-exports')
+    .description('Synchronize package subpath export definitions')
+    .action(lazy(() => import('./commands/packageExports'), 'command'));
+
+  command
+    .command('package-lint-configs')
+    .description(
+      'Migrates all packages to use @backstage/cli/config/eslint-factory',
+    )
+    .action(lazy(() => import('./commands/packageLintConfigs'), 'command'));
+
+  command
+    .command('react-router-deps')
+    .description(
+      'Migrates the react-router dependencies for all packages to be peer dependencies',
+    )
+    .action(lazy(() => import('./commands/reactRouterDeps'), 'command'));
+}
diff --git a/packages/cli/src/commands/versions/utils.ts b/packages/cli/src/modules/migrate/lib/utils.ts
similarity index 97%
rename from packages/cli/src/commands/versions/utils.ts
rename to packages/cli/src/modules/migrate/lib/utils.ts
index 22c5f0c028..5b7b544c87 100644
--- a/packages/cli/src/commands/versions/utils.ts
+++ b/packages/cli/src/modules/migrate/lib/utils.ts
@@ -16,7 +16,7 @@
 
 import ora from 'ora';
 import chalk from 'chalk';
-import { run } from '../../lib/run';
+import { run } from '../../../lib/run';
 
 export async function runYarnInstall() {
   const spinner = ora({