diff --git a/.changeset/silly-spoons-hammer.md b/.changeset/silly-spoons-hammer.md
new file mode 100644
index 00000000000..28fb47dd437
--- /dev/null
+++ b/.changeset/silly-spoons-hammer.md
@@ -0,0 +1,5 @@
+---
+'@shopify/cli-kit': patch
+---
+
+Ignore duplicated plugins to avoid "multiple tunnel plugins" errors
diff --git a/packages/cli-kit/src/public/node/base-command.test.ts b/packages/cli-kit/src/public/node/base-command.test.ts
index 54677ce00de..2ff22d7801c 100644
--- a/packages/cli-kit/src/public/node/base-command.test.ts
+++ b/packages/cli-kit/src/public/node/base-command.test.ts
@@ -559,3 +559,204 @@ const deleteDefaultEnvironment = async (tmpDir: string): Promise<void> => {
   delete clone.environments.default
   await writeFile(joinPath(tmpDir, 'shopify.environments.toml'), encodeTOML({environments: clone} as any))
 }
+
+describe('removeDuplicatedPlugins', () => {
+  let capturedPlugins: Map<string, any> | undefined
+  let outputMock: ReturnType<typeof mockAndCaptureOutput>
+
+  class PluginTestCommand extends MockCommand {
+    async init() {
+      // Set up test plugins before calling super.init()
+      const initialPlugins = capturedPlugins
+      if (initialPlugins) {
+        this.config.plugins = new Map(initialPlugins)
+      }
+
+      const result = await super.init()
+
+      // Capture the plugins after init (which calls removeDuplicatedPlugins)
+      // eslint-disable-next-line require-atomic-updates
+      capturedPlugins = new Map(this.config.plugins)
+
+      return result
+    }
+  }
+
+  beforeEach(() => {
+    capturedPlugins = undefined
+    outputMock = mockAndCaptureOutput()
+    outputMock.clear()
+  })
+
+  test('removes @shopify/app plugin when present', async () => {
+    await inTemporaryDirectory(async (tmpDir) => {
+      // Given - set up plugins to be injected
+      const mockPlugin1 = {name: '@shopify/app', version: '1.0.0'} as any
+      const mockPlugin2 = {name: '@shopify/plugin-ngrok', version: '1.0.0'} as any
+      const mockPlugin3 = {name: '@shopify/plugin-did-you-mean', version: '1.0.0'} as any
+
+      capturedPlugins = new Map([
+        ['@shopify/app', mockPlugin1],
+        ['@shopify/plugin-ngrok', mockPlugin2],
+        ['@shopify/plugin-did-you-mean', mockPlugin3],
+      ])
+
+      // When
+      await PluginTestCommand.run(['--path', tmpDir])
+
+      // Then - verify @shopify/app was removed but others remain
+      expect(capturedPlugins.has('@shopify/app')).toBe(false)
+      expect(capturedPlugins.has('@shopify/plugin-ngrok')).toBe(true)
+      expect(capturedPlugins.has('@shopify/plugin-did-you-mean')).toBe(true)
+      expect(capturedPlugins.size).toBe(2)
+
+      // Verify warning was shown
+      expect(outputMock.output()).toMatch(/Unsupported plugins detected.*@shopify\/app/s)
+      expect(outputMock.output()).toMatch(/shopify plugins remove @shopify\/app/)
+      expect(outputMock.output()).not.toMatch(/shopify plugins remove @shopify\/plugin-cloudflare/)
+    })
+  })
+
+  test('removes @shopify/plugin-cloudflare plugin when present', async () => {
+    await inTemporaryDirectory(async (tmpDir) => {
+      // Given - set up plugins to be injected
+      const mockPlugin1 = {name: '@shopify/plugin-cloudflare', version: '1.0.0'} as any
+      const mockPlugin2 = {name: '@shopify/plugin-ngrok', version: '1.0.0'} as any
+      const mockPlugin3 = {name: '@shopify/plugin-did-you-mean', version: '1.0.0'} as any
+
+      capturedPlugins = new Map([
+        ['@shopify/plugin-cloudflare', mockPlugin1],
+        ['@shopify/plugin-ngrok', mockPlugin2],
+        ['@shopify/plugin-did-you-mean', mockPlugin3],
+      ])
+
+      // When
+      await PluginTestCommand.run(['--path', tmpDir])
+
+      // Then - verify @shopify/plugin-cloudflare was removed but others remain
+      expect(capturedPlugins.has('@shopify/plugin-cloudflare')).toBe(false)
+      expect(capturedPlugins.has('@shopify/plugin-ngrok')).toBe(true)
+      expect(capturedPlugins.has('@shopify/plugin-did-you-mean')).toBe(true)
+      expect(capturedPlugins.size).toBe(2)
+
+      // Verify warning was shown
+      expect(outputMock.output()).toMatch(/Unsupported plugins detected.*@shopify\/plugin-cloudflare/s)
+      expect(outputMock.output()).toMatch(/shopify plugins remove @shopify\/plugin-cloudflare/)
+      expect(outputMock.output()).not.toMatch(/shopify plugins remove @shopify\/app/)
+    })
+  })
+
+  test('removes both @shopify/app and @shopify/plugin-cloudflare plugins when present', async () => {
+    await inTemporaryDirectory(async (tmpDir) => {
+      // Given - set up plugins to be injected
+      const mockPlugin1 = {name: '@shopify/app', version: '1.0.0'} as any
+      const mockPlugin2 = {name: '@shopify/plugin-cloudflare', version: '1.0.0'} as any
+      const mockPlugin3 = {name: '@shopify/plugin-ngrok', version: '1.0.0'} as any
+      const mockPlugin4 = {name: '@shopify/plugin-did-you-mean', version: '1.0.0'} as any
+
+      capturedPlugins = new Map([
+        ['@shopify/app', mockPlugin1],
+        ['@shopify/plugin-cloudflare', mockPlugin2],
+        ['@shopify/plugin-ngrok', mockPlugin3],
+        ['@shopify/plugin-did-you-mean', mockPlugin4],
+      ])
+
+      // When
+      await PluginTestCommand.run(['--path', tmpDir])
+
+      // Then - verify both bundled plugins were removed but others remain
+      expect(capturedPlugins.has('@shopify/app')).toBe(false)
+      expect(capturedPlugins.has('@shopify/plugin-cloudflare')).toBe(false)
+      expect(capturedPlugins.has('@shopify/plugin-ngrok')).toBe(true)
+      expect(capturedPlugins.has('@shopify/plugin-did-you-mean')).toBe(true)
+      expect(capturedPlugins.size).toBe(2)
+
+      // Verify warning was shown with both plugins
+      expect(outputMock.output()).toMatch(/Unsupported plugins detected.*@shopify\/app.*@shopify\/plugin-cloudflare/s)
+      expect(outputMock.output()).toMatch(/shopify plugins remove @shopify\/app/)
+      expect(outputMock.output()).toMatch(/shopify plugins remove @shopify\/plugin-cloudflare/)
+    })
+  })
+
+  test('does not remove any plugins when bundled plugins are not present', async () => {
+    await inTemporaryDirectory(async (tmpDir) => {
+      // Given - set up plugins (none are bundled plugins)
+      const mockPlugin1 = {name: '@shopify/plugin-ngrok', version: '1.0.0'} as any
+      const mockPlugin2 = {name: '@shopify/plugin-did-you-mean', version: '1.0.0'} as any
+      const mockPlugin3 = {name: 'some-other-plugin', version: '1.0.0'} as any
+
+      capturedPlugins = new Map([
+        ['@shopify/plugin-ngrok', mockPlugin1],
+        ['@shopify/plugin-did-you-mean', mockPlugin2],
+        ['some-other-plugin', mockPlugin3],
+      ])
+
+      // When
+      await PluginTestCommand.run(['--path', tmpDir])
+
+      // Then - verify no plugins were removed
+      expect(capturedPlugins.size).toBe(3)
+      expect(capturedPlugins.has('@shopify/plugin-ngrok')).toBe(true)
+      expect(capturedPlugins.has('@shopify/plugin-did-you-mean')).toBe(true)
+      expect(capturedPlugins.has('some-other-plugin')).toBe(true)
+
+      // Verify no warning was shown
+      expect(outputMock.output()).toBe('')
+    })
+  })
+
+  test('handles empty plugin map', async () => {
+    await inTemporaryDirectory(async (tmpDir) => {
+      // Given - empty plugins map
+      capturedPlugins = new Map()
+
+      // When
+      await PluginTestCommand.run(['--path', tmpDir])
+
+      // Then - verify map is still empty
+      expect(capturedPlugins.size).toBe(0)
+
+      // Verify no warning was shown
+      expect(outputMock.output()).toBe('')
+    })
+  })
+
+  test('preserves plugin metadata when removing bundled plugins', async () => {
+    await inTemporaryDirectory(async (tmpDir) => {
+      // Given - set up plugins with more complete metadata
+      const mockPluginApp = {
+        name: '@shopify/app',
+        version: '1.0.0',
+        type: 'core',
+        root: '/path/to/app',
+      } as any
+      const mockPluginTheme = {
+        name: '@shopify/plugin-ngrok',
+        version: '2.0.0',
+        type: 'user',
+        root: '/path/to/theme',
+      } as any
+
+      capturedPlugins = new Map([
+        ['@shopify/app', mockPluginApp],
+        ['@shopify/plugin-ngrok', mockPluginTheme],
+      ])
+
+      // When
+      await PluginTestCommand.run(['--path', tmpDir])
+
+      // Then - verify @shopify/app was removed but theme plugin remains with all its metadata
+      expect(capturedPlugins.has('@shopify/app')).toBe(false)
+      expect(capturedPlugins.has('@shopify/plugin-ngrok')).toBe(true)
+      const remainingPlugin = capturedPlugins.get('@shopify/plugin-ngrok')
+      expect(remainingPlugin).toEqual(mockPluginTheme)
+      expect(remainingPlugin.version).toBe('2.0.0')
+      expect(remainingPlugin.type).toBe('user')
+      expect(remainingPlugin.root).toBe('/path/to/theme')
+
+      // Verify warning was shown
+      expect(outputMock.output()).toMatch(/Unsupported plugins detected.*@shopify\/app/s)
+      expect(outputMock.output()).toMatch(/shopify plugins remove @shopify\/app/)
+    })
+  })
+})
diff --git a/packages/cli-kit/src/public/node/base-command.ts b/packages/cli-kit/src/public/node/base-command.ts
index 0269efed6df..f4236e53e94 100644
--- a/packages/cli-kit/src/public/node/base-command.ts
+++ b/packages/cli-kit/src/public/node/base-command.ts
@@ -12,7 +12,7 @@ import {showNotificationsIfNeeded} from './notifications-system.js'
 import {setCurrentCommandId} from './global-context.js'
 import {JsonMap} from '../../private/common/json.js'
 import {underscore} from '../common/string.js'
-import {Command, Errors} from '@oclif/core'
+import {Command, Config, Errors} from '@oclif/core'
 import {OutputFlags, Input, ParserOutput, FlagInput, OutputArgs} from '@oclif/core/parser'
 
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
@@ -56,6 +56,7 @@ abstract class BaseCommand extends Command {
       // This function runs just prior to `run`
       await registerCleanBugsnagErrorsFromWithinPlugins(this.config)
     }
+    await removeDuplicatedPlugins(this.config)
     this.showNpmFlagWarning()
     await showNotificationsIfNeeded()
     return super.init()
@@ -336,4 +337,22 @@ function commandSupportsFlag(flags: FlagInput | undefined, flagName: string): bo
   return Boolean(flags) && Object.prototype.hasOwnProperty.call(flags, flagName)
 }
 
+async function removeDuplicatedPlugins(config: Config): Promise<void> {
+  const plugins = Array.from(config.plugins.values())
+  const bundlePlugins = ['@shopify/app', '@shopify/plugin-cloudflare']
+  const pluginsToRemove = plugins.filter((plugin) => bundlePlugins.includes(plugin.name))
+  if (pluginsToRemove.length > 0) {
+    const commandsToRun = pluginsToRemove.map((plugin) => `  - shopify plugins remove ${plugin.name}`).join('\n')
+    renderWarning({
+      headline: `Unsupported plugins detected: ${pluginsToRemove.map((plugin) => plugin.name).join(', ')}`,
+      body: [
+        'They are already included in the CLI and installing them as custom plugins can cause conflicts.',
+        `You can fix it by running:\n${commandsToRun}`,
+      ],
+    })
+  }
+  const filteredPlugins = plugins.filter((plugin) => !bundlePlugins.includes(plugin.name))
+  config.plugins = new Map(filteredPlugins.map((plugin) => [plugin.name, plugin]))
+}
+
 export default BaseCommand