diff --git a/.changeset/deploy-config-with-client-id.md b/.changeset/deploy-config-with-client-id.md
new file mode 100644
index 00000000000..5c481dd7897
--- /dev/null
+++ b/.changeset/deploy-config-with-client-id.md
@@ -0,0 +1,5 @@
+---
+'@shopify/app': minor
+---
+
+Allow `--config` and `--client-id` together on `app deploy`, `app dev`, and `app dev clean` to use the selected configuration with a different app
diff --git a/docs-shopify.dev/generated/generated_docs_data_v2.json b/docs-shopify.dev/generated/generated_docs_data_v2.json
index 9931a16c7bf..e32fa234c82 100644
--- a/docs-shopify.dev/generated/generated_docs_data_v2.json
+++ b/docs-shopify.dev/generated/generated_docs_data_v2.json
@@ -908,7 +908,7 @@
           "syntaxKind": "PropertySignature",
           "name": "--client-id <value>",
           "value": "string",
-          "description": "The Client ID of your app.",
+          "description": "The Client ID of your app. Use with --config to deploy that configuration to a different app than the one it is linked to.",
           "isOptional": true,
           "environmentValue": "SHOPIFY_FLAG_CLIENT_ID"
         },
@@ -1021,7 +1021,7 @@
           "environmentValue": "SHOPIFY_FLAG_APP_CONFIG"
         }
       ],
-      "value": "export interface appdeploy {\n  /**\n   * Allows removing extensions and configuration without requiring user confirmation. For CI/CD environments, the recommended flag is --allow-updates. In non-interactive environments, provide this flag, --allow-updates, or --no-release.\n   * @environment SHOPIFY_FLAG_ALLOW_DELETES\n   */\n  '--allow-deletes'?: ''\n\n  /**\n   * Allows adding and updating extensions and configuration without requiring user confirmation. Recommended option for CI/CD environments. In non-interactive environments, provide this flag, --allow-deletes, or --no-release.\n   * @environment SHOPIFY_FLAG_ALLOW_UPDATES\n   */\n  '--allow-updates'?: ''\n\n  /**\n   * Alias of the Shopify account to use for authentication.\n   * @environment SHOPIFY_FLAG_AUTH_ALIAS\n   */\n  '--auth-alias <value>'?: string\n\n  /**\n   * The Client ID of your app.\n   * @environment SHOPIFY_FLAG_CLIENT_ID\n   */\n  '--client-id <value>'?: string\n\n  /**\n   * The name of the app configuration.\n   * @environment SHOPIFY_FLAG_APP_CONFIG\n   */\n  '-c, --config <value>'?: string\n\n  /**\n   * Print the command's JSON schemas.\n   * @environment SHOPIFY_FLAG_JSON_SCHEMA\n   */\n  '--json-schema'?: ''\n\n  /**\n   * Optional message that will be associated with this version. This is for internal use only and won't be available externally.\n   * @environment SHOPIFY_FLAG_MESSAGE\n   */\n  '--message <value>'?: string\n\n  /**\n   * Use with caution: Skips building any elements of the app that require building. You should ensure your app has been prepared in advance, such as by running `shopify app build` or by caching build artifacts.\n   * @environment SHOPIFY_FLAG_NO_BUILD\n   */\n  '--no-build'?: ''\n\n  /**\n   * Disable color output.\n   * @environment SHOPIFY_FLAG_NO_COLOR\n   */\n  '--no-color'?: ''\n\n  /**\n   * Disable interactive prompts and browser authentication.\n   * @environment SHOPIFY_FLAG_NO_INPUT\n   */\n  '--no-input'?: ''\n\n  /**\n   * Creates a version but doesn't release it - it's not made available to merchants. With this flag, a user confirmation is not required. In non-interactive environments, provide this flag, --allow-updates, or --allow-deletes.\n   * @environment SHOPIFY_FLAG_NO_RELEASE\n   */\n  '--no-release'?: ''\n\n  /**\n   * The path to your app directory.\n   * @environment SHOPIFY_FLAG_PATH\n   */\n  '--path <value>'?: string\n\n  /**\n   * Reset all your settings.\n   * @environment SHOPIFY_FLAG_RESET\n   */\n  '--reset'?: ''\n\n  /**\n   * URL associated with the new app version.\n   * @environment SHOPIFY_FLAG_SOURCE_CONTROL_URL\n   */\n  '--source-control-url <value>'?: string\n\n  /**\n   * Increase the verbosity of the output. May include sensitive data.\n   * @environment SHOPIFY_FLAG_VERBOSE\n   */\n  '--verbose'?: ''\n\n  /**\n   * Optional version tag that will be associated with this app version. If not provided, an auto-generated identifier will be generated for this app version.\n   * @environment SHOPIFY_FLAG_VERSION\n   */\n  '--version <value>'?: string\n}"
+      "value": "export interface appdeploy {\n  /**\n   * Allows removing extensions and configuration without requiring user confirmation. For CI/CD environments, the recommended flag is --allow-updates. In non-interactive environments, provide this flag, --allow-updates, or --no-release.\n   * @environment SHOPIFY_FLAG_ALLOW_DELETES\n   */\n  '--allow-deletes'?: ''\n\n  /**\n   * Allows adding and updating extensions and configuration without requiring user confirmation. Recommended option for CI/CD environments. In non-interactive environments, provide this flag, --allow-deletes, or --no-release.\n   * @environment SHOPIFY_FLAG_ALLOW_UPDATES\n   */\n  '--allow-updates'?: ''\n\n  /**\n   * Alias of the Shopify account to use for authentication.\n   * @environment SHOPIFY_FLAG_AUTH_ALIAS\n   */\n  '--auth-alias <value>'?: string\n\n  /**\n   * The Client ID of your app. Use with --config to deploy that configuration to a different app than the one it is linked to.\n   * @environment SHOPIFY_FLAG_CLIENT_ID\n   */\n  '--client-id <value>'?: string\n\n  /**\n   * The name of the app configuration.\n   * @environment SHOPIFY_FLAG_APP_CONFIG\n   */\n  '-c, --config <value>'?: string\n\n  /**\n   * Print the command's JSON schemas.\n   * @environment SHOPIFY_FLAG_JSON_SCHEMA\n   */\n  '--json-schema'?: ''\n\n  /**\n   * Optional message that will be associated with this version. This is for internal use only and won't be available externally.\n   * @environment SHOPIFY_FLAG_MESSAGE\n   */\n  '--message <value>'?: string\n\n  /**\n   * Use with caution: Skips building any elements of the app that require building. You should ensure your app has been prepared in advance, such as by running `shopify app build` or by caching build artifacts.\n   * @environment SHOPIFY_FLAG_NO_BUILD\n   */\n  '--no-build'?: ''\n\n  /**\n   * Disable color output.\n   * @environment SHOPIFY_FLAG_NO_COLOR\n   */\n  '--no-color'?: ''\n\n  /**\n   * Disable interactive prompts and browser authentication.\n   * @environment SHOPIFY_FLAG_NO_INPUT\n   */\n  '--no-input'?: ''\n\n  /**\n   * Creates a version but doesn't release it - it's not made available to merchants. With this flag, a user confirmation is not required. In non-interactive environments, provide this flag, --allow-updates, or --allow-deletes.\n   * @environment SHOPIFY_FLAG_NO_RELEASE\n   */\n  '--no-release'?: ''\n\n  /**\n   * The path to your app directory.\n   * @environment SHOPIFY_FLAG_PATH\n   */\n  '--path <value>'?: string\n\n  /**\n   * Reset all your settings.\n   * @environment SHOPIFY_FLAG_RESET\n   */\n  '--reset'?: ''\n\n  /**\n   * URL associated with the new app version.\n   * @environment SHOPIFY_FLAG_SOURCE_CONTROL_URL\n   */\n  '--source-control-url <value>'?: string\n\n  /**\n   * Increase the verbosity of the output. May include sensitive data.\n   * @environment SHOPIFY_FLAG_VERBOSE\n   */\n  '--verbose'?: ''\n\n  /**\n   * Optional version tag that will be associated with this app version. If not provided, an auto-generated identifier will be generated for this app version.\n   * @environment SHOPIFY_FLAG_VERSION\n   */\n  '--version <value>'?: string\n}"
     }
   },
   "appdevclean": {
@@ -1045,7 +1045,7 @@
           "syntaxKind": "PropertySignature",
           "name": "--client-id <value>",
           "value": "string",
-          "description": "The Client ID of your app.",
+          "description": "The Client ID of your app. Use with --config to clean up the dev preview for a different app than the one it is linked to.",
           "isOptional": true,
           "environmentValue": "SHOPIFY_FLAG_CLIENT_ID"
         },
@@ -1122,7 +1122,7 @@
           "environmentValue": "SHOPIFY_FLAG_STORE"
         }
       ],
-      "value": "export interface appdevclean {\n  /**\n   * Alias of the Shopify account to use for authentication.\n   * @environment SHOPIFY_FLAG_AUTH_ALIAS\n   */\n  '--auth-alias <value>'?: string\n\n  /**\n   * The Client ID of your app.\n   * @environment SHOPIFY_FLAG_CLIENT_ID\n   */\n  '--client-id <value>'?: string\n\n  /**\n   * The name of the app configuration.\n   * @environment SHOPIFY_FLAG_APP_CONFIG\n   */\n  '-c, --config <value>'?: string\n\n  /**\n   * Print the command's JSON schemas.\n   * @environment SHOPIFY_FLAG_JSON_SCHEMA\n   */\n  '--json-schema'?: ''\n\n  /**\n   * Disable color output.\n   * @environment SHOPIFY_FLAG_NO_COLOR\n   */\n  '--no-color'?: ''\n\n  /**\n   * Disable interactive prompts and browser authentication.\n   * @environment SHOPIFY_FLAG_NO_INPUT\n   */\n  '--no-input'?: ''\n\n  /**\n   * The path to your app directory.\n   * @environment SHOPIFY_FLAG_PATH\n   */\n  '--path <value>'?: string\n\n  /**\n   * Reset all your settings.\n   * @environment SHOPIFY_FLAG_RESET\n   */\n  '--reset'?: ''\n\n  /**\n   * Store URL. Must be an existing development store.\n   * @environment SHOPIFY_FLAG_STORE\n   */\n  '-s, --store <value>'?: string\n\n  /**\n   * Increase the verbosity of the output. May include sensitive data.\n   * @environment SHOPIFY_FLAG_VERBOSE\n   */\n  '--verbose'?: ''\n}"
+      "value": "export interface appdevclean {\n  /**\n   * Alias of the Shopify account to use for authentication.\n   * @environment SHOPIFY_FLAG_AUTH_ALIAS\n   */\n  '--auth-alias <value>'?: string\n\n  /**\n   * The Client ID of your app. Use with --config to clean up the dev preview for a different app than the one it is linked to.\n   * @environment SHOPIFY_FLAG_CLIENT_ID\n   */\n  '--client-id <value>'?: string\n\n  /**\n   * The name of the app configuration.\n   * @environment SHOPIFY_FLAG_APP_CONFIG\n   */\n  '-c, --config <value>'?: string\n\n  /**\n   * Print the command's JSON schemas.\n   * @environment SHOPIFY_FLAG_JSON_SCHEMA\n   */\n  '--json-schema'?: ''\n\n  /**\n   * Disable color output.\n   * @environment SHOPIFY_FLAG_NO_COLOR\n   */\n  '--no-color'?: ''\n\n  /**\n   * Disable interactive prompts and browser authentication.\n   * @environment SHOPIFY_FLAG_NO_INPUT\n   */\n  '--no-input'?: ''\n\n  /**\n   * The path to your app directory.\n   * @environment SHOPIFY_FLAG_PATH\n   */\n  '--path <value>'?: string\n\n  /**\n   * Reset all your settings.\n   * @environment SHOPIFY_FLAG_RESET\n   */\n  '--reset'?: ''\n\n  /**\n   * Store URL. Must be an existing development store.\n   * @environment SHOPIFY_FLAG_STORE\n   */\n  '-s, --store <value>'?: string\n\n  /**\n   * Increase the verbosity of the output. May include sensitive data.\n   * @environment SHOPIFY_FLAG_VERBOSE\n   */\n  '--verbose'?: ''\n}"
     }
   },
   "appdev": {
@@ -1155,7 +1155,7 @@
           "syntaxKind": "PropertySignature",
           "name": "--client-id <value>",
           "value": "string",
-          "description": "The Client ID of your app.",
+          "description": "The Client ID of your app. Use with --config to run dev with that configuration for a different app than the one it is linked to.",
           "isOptional": true,
           "environmentValue": "SHOPIFY_FLAG_CLIENT_ID"
         },
@@ -1340,7 +1340,7 @@
           "environmentValue": "SHOPIFY_FLAG_THEME"
         }
       ],
-      "value": "export interface appdev {\n  /**\n   * Alias of the Shopify account to use for authentication.\n   * @environment SHOPIFY_FLAG_AUTH_ALIAS\n   */\n  '--auth-alias <value>'?: string\n\n  /**\n   * Resource URL for checkout UI extension. Format: \"/cart/{productVariantID}:{productQuantity}\"\n   * @environment SHOPIFY_FLAG_CHECKOUT_CART_URL\n   */\n  '--checkout-cart-url <value>'?: string\n\n  /**\n   * The Client ID of your app.\n   * @environment SHOPIFY_FLAG_CLIENT_ID\n   */\n  '--client-id <value>'?: string\n\n  /**\n   * The name of the app configuration.\n   * @environment SHOPIFY_FLAG_APP_CONFIG\n   */\n  '-c, --config <value>'?: string\n\n  /**\n   * Install and use mkcert to generate localhost certificates when --use-localhost is enabled without prompting.\n   * @environment SHOPIFY_FLAG_INSTALL_MKCERT\n   */\n  '--install-mkcert'?: ''\n\n  /**\n   * Print the command's JSON schemas.\n   * @environment SHOPIFY_FLAG_JSON_SCHEMA\n   */\n  '--json-schema'?: ''\n\n  /**\n   * Port to use for localhost. Must be between 1 and 65535.\n   * @environment SHOPIFY_FLAG_LOCALHOST_PORT\n   */\n  '--localhost-port <value>'?: string\n\n  /**\n   * Disable color output.\n   * @environment SHOPIFY_FLAG_NO_COLOR\n   */\n  '--no-color'?: ''\n\n  /**\n   * Disable interactive prompts and browser authentication.\n   * @environment SHOPIFY_FLAG_NO_INPUT\n   */\n  '--no-input'?: ''\n\n  /**\n   * Uses the app URL from the toml file instead an autogenerated URL for dev.\n   * @environment SHOPIFY_FLAG_NO_UPDATE\n   */\n  '--no-update'?: ''\n\n  /**\n   * The file path or URL. The file path is to a file that you want updated on idle. The URL path is where you want a webhook posted to report on file changes.\n   * @environment SHOPIFY_FLAG_NOTIFY\n   */\n  '--notify <value>'?: string\n\n  /**\n   * The path to your app directory.\n   * @environment SHOPIFY_FLAG_PATH\n   */\n  '--path <value>'?: string\n\n  /**\n   * Reset all your settings.\n   * @environment SHOPIFY_FLAG_RESET\n   */\n  '--reset'?: ''\n\n  /**\n   * Skips the installation of dependencies. Deprecated, use workspaces instead.\n   * @environment SHOPIFY_FLAG_SKIP_DEPENDENCIES_INSTALLATION\n   */\n  '--skip-dependencies-installation'?: ''\n\n  /**\n   * Store URL. Must be an existing development or Shopify Plus sandbox store.\n   * @environment SHOPIFY_FLAG_STORE\n   */\n  '-s, --store <value>'?: string\n\n  /**\n   * The password for storefronts with password protection.\n   * @environment SHOPIFY_FLAG_STORE_PASSWORD\n   */\n  '--store-password <value>'?: string\n\n  /**\n   * Resource URL for subscription UI extension. Format: \"/products/{productId}\"\n   * @environment SHOPIFY_FLAG_SUBSCRIPTION_PRODUCT_URL\n   */\n  '--subscription-product-url <value>'?: string\n\n  /**\n   * Theme ID or name of the theme app extension host theme.\n   * @environment SHOPIFY_FLAG_THEME\n   */\n  '-t, --theme <value>'?: string\n\n  /**\n   * Local port of the theme app extension development server. Must be between 1 and 65535.\n   * @environment SHOPIFY_FLAG_THEME_APP_EXTENSION_PORT\n   */\n  '--theme-app-extension-port <value>'?: string\n\n  /**\n   * Use a custom tunnel, it must be running before executing dev. Format: \"https://my-tunnel-url:port\".\n   * @environment SHOPIFY_FLAG_TUNNEL_URL\n   */\n  '--tunnel-url <value>'?: string\n\n  /**\n   * Allow app dev to continue with warnings for eligible app version validation failures.\n   * @environment SHOPIFY_FLAG_UNSAFE_VALIDATION\n   */\n  '--unsafe-validation'?: ''\n\n  /**\n   * Service entry point will listen to localhost. A tunnel won't be used. Will work for testing many app features, but not those that directly invoke your app (E.g: Webhooks)\n   * @environment SHOPIFY_FLAG_USE_LOCALHOST\n   */\n  '--use-localhost'?: ''\n\n  /**\n   * Increase the verbosity of the output. May include sensitive data.\n   * @environment SHOPIFY_FLAG_VERBOSE\n   */\n  '--verbose'?: ''\n}"
+      "value": "export interface appdev {\n  /**\n   * Alias of the Shopify account to use for authentication.\n   * @environment SHOPIFY_FLAG_AUTH_ALIAS\n   */\n  '--auth-alias <value>'?: string\n\n  /**\n   * Resource URL for checkout UI extension. Format: \"/cart/{productVariantID}:{productQuantity}\"\n   * @environment SHOPIFY_FLAG_CHECKOUT_CART_URL\n   */\n  '--checkout-cart-url <value>'?: string\n\n  /**\n   * The Client ID of your app. Use with --config to run dev with that configuration for a different app than the one it is linked to.\n   * @environment SHOPIFY_FLAG_CLIENT_ID\n   */\n  '--client-id <value>'?: string\n\n  /**\n   * The name of the app configuration.\n   * @environment SHOPIFY_FLAG_APP_CONFIG\n   */\n  '-c, --config <value>'?: string\n\n  /**\n   * Install and use mkcert to generate localhost certificates when --use-localhost is enabled without prompting.\n   * @environment SHOPIFY_FLAG_INSTALL_MKCERT\n   */\n  '--install-mkcert'?: ''\n\n  /**\n   * Print the command's JSON schemas.\n   * @environment SHOPIFY_FLAG_JSON_SCHEMA\n   */\n  '--json-schema'?: ''\n\n  /**\n   * Port to use for localhost. Must be between 1 and 65535.\n   * @environment SHOPIFY_FLAG_LOCALHOST_PORT\n   */\n  '--localhost-port <value>'?: string\n\n  /**\n   * Disable color output.\n   * @environment SHOPIFY_FLAG_NO_COLOR\n   */\n  '--no-color'?: ''\n\n  /**\n   * Disable interactive prompts and browser authentication.\n   * @environment SHOPIFY_FLAG_NO_INPUT\n   */\n  '--no-input'?: ''\n\n  /**\n   * Uses the app URL from the toml file instead an autogenerated URL for dev.\n   * @environment SHOPIFY_FLAG_NO_UPDATE\n   */\n  '--no-update'?: ''\n\n  /**\n   * The file path or URL. The file path is to a file that you want updated on idle. The URL path is where you want a webhook posted to report on file changes.\n   * @environment SHOPIFY_FLAG_NOTIFY\n   */\n  '--notify <value>'?: string\n\n  /**\n   * The path to your app directory.\n   * @environment SHOPIFY_FLAG_PATH\n   */\n  '--path <value>'?: string\n\n  /**\n   * Reset all your settings.\n   * @environment SHOPIFY_FLAG_RESET\n   */\n  '--reset'?: ''\n\n  /**\n   * Skips the installation of dependencies. Deprecated, use workspaces instead.\n   * @environment SHOPIFY_FLAG_SKIP_DEPENDENCIES_INSTALLATION\n   */\n  '--skip-dependencies-installation'?: ''\n\n  /**\n   * Store URL. Must be an existing development or Shopify Plus sandbox store.\n   * @environment SHOPIFY_FLAG_STORE\n   */\n  '-s, --store <value>'?: string\n\n  /**\n   * The password for storefronts with password protection.\n   * @environment SHOPIFY_FLAG_STORE_PASSWORD\n   */\n  '--store-password <value>'?: string\n\n  /**\n   * Resource URL for subscription UI extension. Format: \"/products/{productId}\"\n   * @environment SHOPIFY_FLAG_SUBSCRIPTION_PRODUCT_URL\n   */\n  '--subscription-product-url <value>'?: string\n\n  /**\n   * Theme ID or name of the theme app extension host theme.\n   * @environment SHOPIFY_FLAG_THEME\n   */\n  '-t, --theme <value>'?: string\n\n  /**\n   * Local port of the theme app extension development server. Must be between 1 and 65535.\n   * @environment SHOPIFY_FLAG_THEME_APP_EXTENSION_PORT\n   */\n  '--theme-app-extension-port <value>'?: string\n\n  /**\n   * Use a custom tunnel, it must be running before executing dev. Format: \"https://my-tunnel-url:port\".\n   * @environment SHOPIFY_FLAG_TUNNEL_URL\n   */\n  '--tunnel-url <value>'?: string\n\n  /**\n   * Allow app dev to continue with warnings for eligible app version validation failures.\n   * @environment SHOPIFY_FLAG_UNSAFE_VALIDATION\n   */\n  '--unsafe-validation'?: ''\n\n  /**\n   * Service entry point will listen to localhost. A tunnel won't be used. Will work for testing many app features, but not those that directly invoke your app (E.g: Webhooks)\n   * @environment SHOPIFY_FLAG_USE_LOCALHOST\n   */\n  '--use-localhost'?: ''\n\n  /**\n   * Increase the verbosity of the output. May include sensitive data.\n   * @environment SHOPIFY_FLAG_VERBOSE\n   */\n  '--verbose'?: ''\n}"
     }
   },
   "appenvpull": {
diff --git a/packages/app/src/cli/commands/app/deploy.test.ts b/packages/app/src/cli/commands/app/deploy.test.ts
new file mode 100644
index 00000000000..75918029e0e
--- /dev/null
+++ b/packages/app/src/cli/commands/app/deploy.test.ts
@@ -0,0 +1,47 @@
+import Deploy from './deploy.js'
+import {deploy} from '../../services/deploy.js'
+import {linkedAppContext} from '../../services/app-context.js'
+import {testAppLinked, testOrganizationApp} from '../../models/app/app.test-data.js'
+import {inTemporaryDirectory} from '@shopify/cli-kit/node/fs'
+import {beforeEach, describe, expect, test, vi} from 'vitest'
+
+vi.mock('../../services/deploy.js')
+vi.mock('../../services/app-context.js')
+
+describe('app deploy command', () => {
+  beforeEach(() => {
+    vi.mocked(linkedAppContext).mockReset()
+    const app = testAppLinked()
+    vi.mocked(linkedAppContext).mockResolvedValue({
+      app,
+      remoteApp: testOrganizationApp(),
+    } as Awaited<ReturnType<typeof linkedAppContext>>)
+    vi.mocked(deploy).mockResolvedValue({app} as Awaited<ReturnType<typeof deploy>>)
+  })
+
+  test('accepts --config together with --client-id to deploy a configuration to a different app', async () => {
+    await inTemporaryDirectory(async (tmp) => {
+      await Deploy.run(
+        ['--path', tmp, '--config', 'prod', '--client-id', 'a-different-app', '--allow-updates'],
+        import.meta.url,
+      )
+
+      expect(linkedAppContext).toHaveBeenCalledWith({
+        directory: tmp,
+        clientId: 'a-different-app',
+        forceRelink: false,
+        userProvidedConfigName: 'prod',
+      })
+    })
+  })
+
+  test('still rejects --reset together with --config', async () => {
+    await inTemporaryDirectory(async (tmp) => {
+      await expect(
+        Deploy.run(['--path', tmp, '--config', 'prod', '--reset', '--allow-updates'], import.meta.url),
+      ).rejects.toThrow()
+
+      expect(linkedAppContext).not.toHaveBeenCalled()
+    })
+  })
+})
diff --git a/packages/app/src/cli/commands/app/deploy.ts b/packages/app/src/cli/commands/app/deploy.ts
index 4eee47e7100..d22bdd58f49 100644
--- a/packages/app/src/cli/commands/app/deploy.ts
+++ b/packages/app/src/cli/commands/app/deploy.ts
@@ -25,6 +25,14 @@ export default class Deploy extends AppLinkedCommand {
   static flags = {
     ...globalFlags,
     ...appFlags,
+    // Unlike the shared app flag, deploy accepts --client-id together with --config:
+    // the configuration selected by --config is deployed to the app identified by --client-id.
+    'client-id': Flags.string({
+      hidden: false,
+      description:
+        'The Client ID of your app. Use with --config to deploy that configuration to a different app than the one it is linked to.',
+      env: 'SHOPIFY_FLAG_CLIENT_ID',
+    }),
     'allow-updates': Flags.boolean({
       hidden: false,
       description:
diff --git a/packages/app/src/cli/commands/app/dev.test.ts b/packages/app/src/cli/commands/app/dev.test.ts
index 5bd68660525..f14870d69fa 100644
--- a/packages/app/src/cli/commands/app/dev.test.ts
+++ b/packages/app/src/cli/commands/app/dev.test.ts
@@ -1,4 +1,6 @@
 import Dev from './dev.js'
+import DevClean from './dev/clean.js'
+import {devClean} from '../../services/dev-clean.js'
 import {dev} from '../../services/dev.js'
 import {linkedAppContext} from '../../services/app-context.js'
 import {storeContext} from '../../services/store-context.js'
@@ -17,6 +19,7 @@ import {addPublicMetadata} from '@shopify/cli-kit/node/metadata'
 import {beforeEach, describe, expect, test, vi} from 'vitest'
 
 vi.mock('../../services/dev.js')
+vi.mock('../../services/dev-clean.js')
 vi.mock('../../services/app-context.js')
 vi.mock('../../services/store-context.js')
 vi.mock('../../services/dev/tunnel-mode.js')
@@ -51,6 +54,42 @@ describe('app dev command', () => {
     return {store}
   }
 
+  test.each([
+    ['app dev', Dev, dev],
+    ['app dev clean', DevClean, devClean],
+  ])('%s accepts --config together with --client-id', async (_name, command, service) => {
+    await inTemporaryDirectory(async (tmp) => {
+      const {store} = mockAppAndStore(tmp)
+      vi.mocked(getTunnelMode).mockResolvedValue({mode: 'auto'})
+
+      await command.run(
+        ['--path', tmp, '--store', store.shopDomain, '--config', 'prod', '--client-id', 'a-different-app'],
+        import.meta.url,
+      )
+
+      expect(linkedAppContext).toHaveBeenCalledWith({
+        directory: tmp,
+        clientId: 'a-different-app',
+        forceRelink: false,
+        userProvidedConfigName: 'prod',
+      })
+      expect(service).toHaveBeenCalled()
+    })
+  })
+
+  test.each([
+    ['app dev', Dev],
+    ['app dev clean', DevClean],
+  ])('%s still rejects --reset together with --config', async (_name, command) => {
+    await inTemporaryDirectory(async (tmp) => {
+      await expect(command.run(['--path', tmp, '--config', 'prod', '--reset'], import.meta.url)).rejects.toThrow()
+
+      expect(linkedAppContext).not.toHaveBeenCalled()
+      expect(dev).not.toHaveBeenCalled()
+      expect(devClean).not.toHaveBeenCalled()
+    })
+  })
+
   test('does not require --use-localhost when --install-mkcert is not passed', async () => {
     await inTemporaryDirectory(async (tmp) => {
       const {store} = mockAppAndStore(tmp)
@@ -113,6 +152,7 @@ describe('app dev command', () => {
       await expect(Dev.run(['--path', tmp, '--install-mkcert'], import.meta.url)).rejects.toThrow()
 
       expect(dev).not.toHaveBeenCalled()
+      expect(devClean).not.toHaveBeenCalled()
     })
   })
 })
diff --git a/packages/app/src/cli/commands/app/dev.ts b/packages/app/src/cli/commands/app/dev.ts
index 1b0de21e116..6fe12af0385 100644
--- a/packages/app/src/cli/commands/app/dev.ts
+++ b/packages/app/src/cli/commands/app/dev.ts
@@ -24,6 +24,13 @@ export default class Dev extends AppLinkedCommand {
   static flags = {
     ...globalFlags,
     ...appFlags,
+    // The selected configuration is used with the app identified by --client-id.
+    'client-id': Flags.string({
+      hidden: false,
+      description:
+        'The Client ID of your app. Use with --config to run dev with that configuration for a different app than the one it is linked to.',
+      env: 'SHOPIFY_FLAG_CLIENT_ID',
+    }),
     store: Flags.string({
       char: 's',
       description: 'Store URL. Must be an existing development or Shopify Plus sandbox store.',
diff --git a/packages/app/src/cli/commands/app/dev/clean.ts b/packages/app/src/cli/commands/app/dev/clean.ts
index 6b87c55a849..c4c78c56772 100644
--- a/packages/app/src/cli/commands/app/dev/clean.ts
+++ b/packages/app/src/cli/commands/app/dev/clean.ts
@@ -20,6 +20,12 @@ export default class DevClean extends AppLinkedCommand {
   static flags = {
     ...globalFlags,
     ...appFlags,
+    'client-id': Flags.string({
+      hidden: false,
+      description:
+        'The Client ID of your app. Use with --config to clean up the dev preview for a different app than the one it is linked to.',
+      env: 'SHOPIFY_FLAG_CLIENT_ID',
+    }),
     store: Flags.string({
       hidden: false,
       char: 's',
diff --git a/packages/app/src/cli/models/app/app.ts b/packages/app/src/cli/models/app/app.ts
index 73eec01f3fc..b101e37125b 100644
--- a/packages/app/src/cli/models/app/app.ts
+++ b/packages/app/src/cli/models/app/app.ts
@@ -194,6 +194,8 @@ export interface AppConfigurationInterface<
   directory: string
   configPath: string
   configuration: TConfig
+  /** The client ID provided by the command, preserved when the app reloads. */
+  readonly clientIdOverride?: string
   configSchema: SchemaForConfig<TConfig>
   specifications: TModuleSpec[]
   remoteFlags: Flag[]
@@ -277,6 +279,7 @@ export class App<
   directory: string
   configPath: string
   configuration: TConfig
+  readonly clientIdOverride?: string
   webs: Web[]
   dotenv?: DotEnvFile
   errors: AppErrors
@@ -292,6 +295,7 @@ export class App<
     directory,
     configPath,
     configuration,
+    clientIdOverride,
     webs,
     modules,
     dotenv,
@@ -306,6 +310,7 @@ export class App<
     this.directory = directory
     this.configPath = configPath
     this.configuration = configuration
+    this.clientIdOverride = clientIdOverride
     this.webs = webs
     this.dotenv = dotenv
     this.realExtensions = modules
diff --git a/packages/app/src/cli/models/app/loader.ts b/packages/app/src/cli/models/app/loader.ts
index 28bac00d9d4..8c240700171 100644
--- a/packages/app/src/cli/models/app/loader.ts
+++ b/packages/app/src/cli/models/app/loader.ts
@@ -140,7 +140,7 @@ export function parseConfigurationObject<TSchema extends zod.ZodType>(
 /**
  * Parses a configuration object using a specification's schema, and returns a result.
  */
-export function parseConfigurationObjectAgainstSpecification<TSchema extends zod.ZodType>(
+function parseConfigurationObjectAgainstSpecification<TSchema extends zod.ZodType>(
   spec: ExtensionSpecification,
   filepath: string,
   configurationObject: object,
@@ -340,6 +340,7 @@ export async function loadAppFromContext<TModuleSpec extends ExtensionSpecificat
     configPath: configurationPath,
     configuration,
     configurationLoadResultMetadata,
+    clientIdOverride,
     configSchema,
     specifications,
     remoteFlags,
@@ -456,6 +457,7 @@ export async function reloadApp(app: AppLinkedInterface): Promise<AppLinkedInter
     specifications: app.specifications,
     remoteFlags: app.remoteFlags ?? [],
     reloadState,
+    clientIdOverride: app.clientIdOverride,
   })
   if (!newApp.errors.isEmpty()) {
     const errors = newApp.errors.getErrors()
@@ -529,6 +531,7 @@ class AppLoader<TConfig extends CurrentAppConfiguration, TModuleSpec extends Ext
       directory,
       configPath,
       configuration,
+      clientIdOverride: this.loadedConfiguration.clientIdOverride,
       webs,
       modules: extensions,
       dotenv,
diff --git a/packages/app/src/cli/services/app-context.test.ts b/packages/app/src/cli/services/app-context.test.ts
index 95fe5c3ea0b..e5572467ad6 100644
--- a/packages/app/src/cli/services/app-context.test.ts
+++ b/packages/app/src/cli/services/app-context.test.ts
@@ -3,6 +3,7 @@ import {fetchSpecifications} from './generate/fetch-extension-specifications.js'
 import {addUidToTomlsIfNecessary} from './app/add-uid-to-extension-toml.js'
 import link from './app/config/link.js'
 import {appFromIdentifiers} from './context.js'
+import {handleWatcherEvents} from './dev/app-events/app-event-watcher-handler.js'
 
 import * as localStorage from './local-storage.js'
 import {fetchOrgFromId} from './dev/fetch.js'
@@ -11,9 +12,10 @@ import metadata from '../metadata.js'
 import * as loader from '../models/app/loader.js'
 import {loadLocalExtensionsSpecifications} from '../models/extensions/load-specifications.js'
 import {beforeEach, describe, expect, test, vi} from 'vitest'
-import {inTemporaryDirectory, writeFile, mkdir} from '@shopify/cli-kit/node/fs'
+import {inTemporaryDirectory, writeFile, mkdir, readFile} from '@shopify/cli-kit/node/fs'
 import {joinPath, normalizePath} from '@shopify/cli-kit/node/path'
 import {tryParseInt} from '@shopify/cli-kit/common/string'
+import {AbortController} from '@shopify/cli-kit/node/abort'
 
 vi.mock('../models/app/validation/multi-cli-warning.js')
 vi.mock('./generate/fetch-extension-specifications.js')
@@ -145,6 +147,150 @@ client_id="test-api-key"`
     })
   })
 
+  test.each([true, false])(
+    'keeps the selected configuration and target client ID after reload (matching TOML: %s)',
+    async (hasMatchingConfig) => {
+      await inTemporaryDirectory(async (tmp) => {
+        const sourceConfig = `
+name = "production-app"
+client_id = "source-client-id"
+application_url = "https://production.example.com"
+embedded = true
+
+[access_scopes]
+scopes = "read_products"
+
+[webhooks]
+api_version = "2026-07"
+
+[auth]
+redirect_urls = ["https://production.example.com/auth"]
+`
+        const targetConfig = `
+name = "development-app"
+client_id = "target-client-id"
+application_url = "https://development.example.com"
+embedded = true
+`
+        const sourceConfigPath = joinPath(tmp, 'shopify.app.prod.toml')
+        const targetConfigPath = joinPath(tmp, 'shopify.app.dev.toml')
+        await writeAppConfig(tmp, sourceConfig, 'shopify.app.prod.toml')
+        if (hasMatchingConfig) {
+          await writeFile(targetConfigPath, targetConfig)
+          localStorage.setCachedAppInfo({directory: tmp, configFile: 'shopify.app.dev.toml'})
+        }
+        await mkdir(joinPath(tmp, '.shopify'))
+        await writeFile(
+          joinPath(tmp, '.shopify', 'project.json'),
+          JSON.stringify({
+            'source-client-id': {dev_store_url: 'source.myshopify.com'},
+            'target-client-id': {dev_store_url: 'target.myshopify.com'},
+          }),
+        )
+        const functionDirectory = joinPath(tmp, 'extensions', 'discount')
+        await mkdir(functionDirectory)
+        await writeFile(
+          joinPath(functionDirectory, 'shopify.extension.toml'),
+          `api_version = "2026-07"
+
+[[extensions]]
+name = "Discount"
+handle = "discount"
+type = "function"
+`,
+        )
+        const {loadLocalExtensionsSpecifications: loadSpecifications} = await vi.importActual<
+          typeof import('../models/extensions/load-specifications.js')
+        >('../models/extensions/load-specifications.js')
+        vi.mocked(fetchSpecifications).mockResolvedValue(
+          (await loadSpecifications()).map((specification) => ({...specification, loadedRemoteSpecs: true})),
+        )
+        vi.mocked(appFromIdentifiers).mockResolvedValue({...mockRemoteApp, apiKey: 'target-client-id'})
+
+        const {app} = await linkedAppContext({
+          directory: tmp,
+          clientId: 'target-client-id',
+          forceRelink: false,
+          userProvidedConfigName: 'prod',
+        })
+
+        expect(appFromIdentifiers).toHaveBeenCalledWith({apiKey: 'target-client-id'})
+        expect(link).not.toHaveBeenCalled()
+        expect(app.configPath).toBe(normalizePath(sourceConfigPath))
+        expect(app.configuration).toEqual(
+          expect.objectContaining({
+            client_id: 'target-client-id',
+            name: 'production-app',
+            application_url: 'https://production.example.com',
+            access_scopes: {scopes: 'read_products'},
+          }),
+        )
+        expect(app.hiddenConfig.dev_store_url).toBe('target.myshopify.com')
+
+        const reloadedApp = await loader.reloadApp(app)
+
+        expect(reloadedApp.configPath).toBe(app.configPath)
+        expect(reloadedApp.configuration).toEqual(app.configuration)
+        expect(reloadedApp.hiddenConfig.dev_store_url).toBe('target.myshopify.com')
+        expect((await reloadedApp.manifest(undefined)).modules).toEqual(
+          expect.arrayContaining([
+            expect.objectContaining({
+              handle: 'discount',
+              config: expect.objectContaining({app_key: 'target-client-id'}),
+            }),
+          ]),
+        )
+        expect(reloadedApp.clientIdOverride).toBe('target-client-id')
+        await expect(readFile(sourceConfigPath)).resolves.toBe(sourceConfig)
+        const updatedConfig = sourceConfig.replace('production-app', 'updated-app')
+        await writeFile(sourceConfigPath, updatedConfig)
+        const event = await handleWatcherEvents(
+          [{type: 'extensions_config_updated', path: sourceConfigPath, extensionPath: tmp, startTime: [0, 0]}],
+          reloadedApp,
+          {stdout: process.stdout, stderr: process.stderr, signal: new AbortController().signal},
+        )
+        expect(event?.appWasReloaded).toBe(true)
+        expect(event?.app.configuration.client_id).toBe('target-client-id')
+        expect(event?.app.configuration.name).toBe('updated-app')
+        expect(event?.app.clientIdOverride).toBe('target-client-id')
+        expect(event?.app.hiddenConfig.dev_store_url).toBe('target.myshopify.com')
+        expect((await event!.app.manifest(undefined)).modules).toEqual(
+          expect.arrayContaining([
+            expect.objectContaining({
+              handle: 'discount',
+              config: expect.objectContaining({app_key: 'target-client-id'}),
+            }),
+          ]),
+        )
+        await expect(readFile(sourceConfigPath)).resolves.toBe(updatedConfig)
+        if (hasMatchingConfig) await expect(readFile(targetConfigPath)).resolves.toBe(targetConfig)
+      })
+    },
+  )
+
+  test.each([
+    {clientId: undefined, expectedClientId: 'updated-client-id'},
+    {clientId: 'source-client-id', expectedClientId: 'source-client-id'},
+  ])('reload uses $expectedClientId when the provided client ID is $clientId', async ({clientId, expectedClientId}) => {
+    await inTemporaryDirectory(async (tmp) => {
+      const content = 'name = "test-app"\nclient_id = "source-client-id"\n'
+      await writeAppConfig(tmp, content)
+      vi.mocked(appFromIdentifiers).mockResolvedValue({...mockRemoteApp, apiKey: 'source-client-id'})
+      const {app} = await linkedAppContext({
+        directory: tmp,
+        clientId,
+        forceRelink: false,
+        userProvidedConfigName: undefined,
+      })
+      await writeAppConfig(tmp, content.replace('source-client-id', 'updated-client-id'))
+
+      const reloadedApp = await loader.reloadApp(app)
+
+      expect(reloadedApp.configuration.client_id).toBe(expectedClientId)
+      expect(reloadedApp.clientIdOverride).toBe(clientId)
+    })
+  })
+
   test('resets app when there is a valid toml but reset option is true', async () => {
     await inTemporaryDirectory(async (tmp) => {
       // Given
diff --git a/packages/app/src/cli/services/app-context.ts b/packages/app/src/cli/services/app-context.ts
index 00d37b86fce..d2d84124a14 100644
--- a/packages/app/src/cli/services/app-context.ts
+++ b/packages/app/src/cli/services/app-context.ts
@@ -136,7 +136,7 @@ export async function linkedAppContext({
     activeConfig,
     specifications,
     remoteFlags: remoteApp.flags,
-    clientIdOverride: clientId && clientId !== configClientId ? clientId : undefined,
+    clientIdOverride: clientId,
   })
 
   if (!unsafeTolerateErrors && !localApp.errors.isEmpty()) {
diff --git a/packages/app/src/cli/services/deploy.test.ts b/packages/app/src/cli/services/deploy.test.ts
index 619710f1043..49e2063611c 100644
--- a/packages/app/src/cli/services/deploy.test.ts
+++ b/packages/app/src/cli/services/deploy.test.ts
@@ -808,6 +808,7 @@ describe('ImportExtensionsIfNeeded', () => {
       developerPlatformClient,
       extensions: mockExtensions,
     })
+    expect(reloadApp).toHaveBeenCalledWith(app)
     expect(result).toBe(reloadedApp)
   })
 
diff --git a/packages/cli/README.md b/packages/cli/README.md
index 88184dfa59d..e0dfaf08d02 100644
--- a/packages/cli/README.md
+++ b/packages/cli/README.md
@@ -637,9 +637,9 @@ Deploy your Shopify app.
 
 ```
 USAGE
-  $ shopify app deploy [--auth-alias <value>] [--client-id <value> | -c <value>] [--json-schema] [--message
-    <value>] [--no-build] [--no-color] [--no-input] [--no-release | --allow-updates | --allow-deletes] [--path <value>]
-    [--reset | ] [--source-control-url <value>] [--verbose] [--version <value>]
+  $ shopify app deploy [--auth-alias <value>] [--client-id <value>] [--json-schema] [--message <value>]
+    [--no-build] [--no-color] [--no-input] [--no-release | --allow-updates | --allow-deletes] [--path <value>] [--reset
+    | -c <value>] [--source-control-url <value>] [--verbose] [--version <value>]
 
 FLAGS
   -c, --config=<value>
@@ -662,7 +662,8 @@ FLAGS
       [env: SHOPIFY_FLAG_AUTH_ALIAS]
 
   --client-id=<value>
-      The Client ID of your app.
+      The Client ID of your app. Use with --config to deploy that configuration to a different app than the one it is
+      linked to.
       [env: SHOPIFY_FLAG_CLIENT_ID]
 
   --json-schema
@@ -732,11 +733,11 @@ Run the app.
 
 ```
 USAGE
-  $ shopify app dev [--auth-alias <value>] [--checkout-cart-url <value>] [--client-id <value> | -c <value>]
+  $ shopify app dev [--auth-alias <value>] [--checkout-cart-url <value>] [--client-id <value>]
     [--install-mkcert --use-localhost] [--json-schema] [--localhost-port <value>] [--no-color] [--no-input]
-    [--no-update] [--notify <value>] [--path <value>] [--reset | ] [--skip-dependencies-installation] [-s <value>]
-    [--store-password <value>] [--subscription-product-url <value>] [-t <value>] [--theme-app-extension-port <value>]
-    [--tunnel-url <value> | ] [--unsafe-validation] [--verbose]
+    [--no-update] [--notify <value>] [--path <value>] [--reset | -c <value>] [--skip-dependencies-installation] [-s
+    <value>] [--store-password <value>] [--subscription-product-url <value>] [-t <value>] [--theme-app-extension-port
+    <value>] [--tunnel-url <value> | ] [--unsafe-validation] [--verbose]
 
 FLAGS
   -c, --config=<value>
@@ -760,7 +761,8 @@ FLAGS
       [env: SHOPIFY_FLAG_CHECKOUT_CART_URL]
 
   --client-id=<value>
-      The Client ID of your app.
+      The Client ID of your app. Use with --config to run dev with that configuration for a different app than the one it
+      is linked to.
       [env: SHOPIFY_FLAG_CLIENT_ID]
 
   --install-mkcert
@@ -846,8 +848,8 @@ Cleans up the dev preview from the selected store.
 
 ```
 USAGE
-  $ shopify app dev clean [--auth-alias <value>] [--client-id <value> | -c <value>] [--json-schema] [--no-color]
-    [--no-input] [--path <value>] [--reset | ] [-s <value>] [--verbose]
+  $ shopify app dev clean [--auth-alias <value>] [--client-id <value>] [--json-schema] [--no-color] [--no-input]
+    [--path <value>] [--reset | -c <value>] [-s <value>] [--verbose]
 
 FLAGS
   -c, --config=<value>
@@ -863,7 +865,8 @@ FLAGS
       [env: SHOPIFY_FLAG_AUTH_ALIAS]
 
   --client-id=<value>
-      The Client ID of your app.
+      The Client ID of your app. Use with --config to clean up the dev preview for a different app than the one it is
+      linked to.
       [env: SHOPIFY_FLAG_CLIENT_ID]
 
   --json-schema
diff --git a/packages/cli/oclif.manifest.json b/packages/cli/oclif.manifest.json
index a531ad3df4a..65c22767600 100644
--- a/packages/cli/oclif.manifest.json
+++ b/packages/cli/oclif.manifest.json
@@ -990,11 +990,8 @@
           "type": "option"
         },
         "client-id": {
-          "description": "The Client ID of your app.",
+          "description": "The Client ID of your app. Use with --config to deploy that configuration to a different app than the one it is linked to.",
           "env": "SHOPIFY_FLAG_CLIENT_ID",
-          "exclusive": [
-            "config"
-          ],
           "hasDynamicHelp": false,
           "hidden": false,
           "multiple": false,
@@ -1144,11 +1141,8 @@
           "type": "option"
         },
         "client-id": {
-          "description": "The Client ID of your app.",
+          "description": "The Client ID of your app. Use with --config to run dev with that configuration for a different app than the one it is linked to.",
           "env": "SHOPIFY_FLAG_CLIENT_ID",
-          "exclusive": [
-            "config"
-          ],
           "hasDynamicHelp": false,
           "hidden": false,
           "multiple": false,
@@ -1372,11 +1366,8 @@
           "type": "option"
         },
         "client-id": {
-          "description": "The Client ID of your app.",
+          "description": "The Client ID of your app. Use with --config to clean up the dev preview for a different app than the one it is linked to.",
           "env": "SHOPIFY_FLAG_CLIENT_ID",
-          "exclusive": [
-            "config"
-          ],
           "hasDynamicHelp": false,
           "hidden": false,
           "multiple": false,