Shopify CLI always references deleted app client_id — cannot run or link any new app

I have reproduced the issue on the latest CLI version.

Yes, I am on the latest version

I have searched existing posts and this report is not a duplicate.

Yes, this isn’t a duplicate

In which of these areas are you experiencing a problem?

App

Expected behavior

Shopify CLI should connect and run any app using its own shopify.app.toml configuration and its own client_id, independent of other apps.

Actual behavior

When running shopify app dev (even with --reset), the CLI throws:

No app with client ID <some_other_app_id> found

The referenced client_id belongs to an old app that was deleted, yet the CLI still tries to use it.

Reproduction steps

  1. Create a new app in the Partner Dashboard.
  2. Run shopify app config link → select or create the new app.
  3. Run shopify app dev or shopify app dev --reset.

Verbose output

2025-10-24T10:55:43.007Z: Running command app dev
2025-10-24T10:55:43.022Z: Running system process:
· Command: C:\nvm4w\nodejs\node.exe C:\nvm4w\nodejs\node_modules@shopify\cli\bin\run.js notifications list --ignore-errors
· Working directory: E:/Work_Web/Shopify/new_app/lean-vertical-app

2025-10-24T10:55:43.039Z: Notifications to show: 0
╭─ warning ────────────────────────────────────────────────────────────────────────────────╮
│                                                                                          │
│  The flag api-key has been deprecated in favor of client-id                          │
│                                                                                          │
╰──────────────────────────────────────────────────────────────────────────────────────────╯

2025-10-24T10:55:43.106Z: Reading cached app information for directory E:/Work_Web/Shopify/new_app/lean-vertical-app…
2025-10-24T10:55:43.109Z: Reading the content of file at shopify.app.toml…
2025-10-24T10:55:43.115Z: Reading the content of file at shopify.app.toml…
2025-10-24T10:55:43.119Z: Reading cached app information for directory E:/Work_Web/Shopify/new_app/lean-vertical-app…
2025-10-24T10:55:43.120Z: Reading the content of file at shopify.app.toml…
2025-10-24T10:55:43.123Z: Reading the content of file at shopify.app.toml…
2025-10-24T10:55:43.130Z: Reading the content of file at .gitignore…
2025-10-24T10:55:43.143Z: Reading the content of file at package.json…
2025-10-24T10:55:43.145Z: Reading the content of file at package.json…
2025-10-24T10:55:43.187Z: Running system process:
· Command: npm prefix
· Working directory: E:/Work_Web/Shopify/new_app/lean-vertical-app

2025-10-24T10:55:43.676Z: Obtaining the dependency manager in directory E:\Work_Web\Shopify\new_app\lean-vertical-app…
2025-10-24T10:55:43.678Z: Reading the content of file at package.json…
2025-10-24T10:55:43.680Z: Reading the content of file at .shopify/project.json…
2025-10-24T10:55:43.688Z: Reading the content of file at shopify.web.toml…
2025-10-24T10:55:43.694Z: Notifications to show: 0
2025-10-24T10:55:43.699Z: Ensuring that the user is authenticated with the App Management API with the following scopes:



2025-10-24T10:55:43.700Z: Getting session store…
2025-10-24T10:55:43.702Z: Getting current session ID…
2025-10-24T10:55:43.703Z: Validating existing session against the scopes:
[
“openid”,
“https:// api.shopify .com/auth/shop.admin.graphql”,
“https:// api.shopify .com/auth/shop.admin.themes”,
“https:// api.shopify .com/auth/partners.collaborator-relationships.readonly”,
“https:// api.shopify .com/auth/shop.storefront-renderer.devtools”,
“https:// api.shopify .com/auth/partners.app.cli.access”,
“https:// api.shopify .com/auth/destinations.readonly”,
“https:// api.shopify .com/auth/organization.store-management”,
“https:// api.shopify .com/auth/organization.on-demand-user-access”,
“https:// api.shopify .com/auth/organization.apps.manage”
]
For applications:
{
“appManagementApi”: {
“scopes”: 

},
“businessPlatformApi”: {
“scopes”: 

}
}

2025-10-24T10:55:43.704Z: - Token validation → It’s expired: false
2025-10-24T10:55:43.708Z: Sending “BusinessPlatform” GraphQL request:
query UserInfo {
currentUserAccount {
uuid
email
organizations(first: 2) {
nodes {
name
__typename
}
__typename
}
__typename
}
}

With request headers:

User-Agent: Shopify CLI; v=3.86.1

Keep-Alive: timeout=30

Sec-CH-UA-PLATFORM: win32

Content-Type: application/json

to https:// destinations.shopifysvc .com/destinations/api/2020-07/graphql
2025-10-24T10:55:43.762Z: Sending “App Management” GraphQL request:
query ActiveAppReleaseFromApiKey($apiKey: String!) {
app: appByKey(key: $apiKey) {
…AppVersionInfo
__typename
}
}

fragment ReleasedAppModule on AppModule {
uuid
userIdentifier
handle
config
target
specification {
identifier
externalIdentifier
name
managementExperience
}
}

fragment AppVersionInfo on App {
id
key
organizationId
activeRoot {
clientCredentials {
secrets {
key
}
}
grantedShopifyApprovalScopes
}
activeRelease {
id
version {
name
appModules {
…ReleasedAppModule
}
}
}
}

With variables:
{
“apiKey”: “*****”
}

With request headers:

User-Agent: Shopify CLI; v=3.86.1

Keep-Alive: timeout=30

Sec-CH-UA-PLATFORM: win32

Content-Type: application/json

to https: //app.shopify .com/app_management/unstable/graphql.json
2025-10-24T10:55:44.159Z: Request to https: //app.shopify .com/app_management/unstable/graphql.json completed in 395 ms
With response headers:

content-type: application/json; charset=utf-8

server-timing: processing;dur=92, verdict_flag_enabled;desc=“count=2”;dur=0.178, _y;desc=“bd6b4fd3-0ff0-40af-b5c5-48a27b2b945c”, _s;desc=“fe8da3fe-338e-4846-8287-b1a4cd6c6134”, cfRequestDuration;dur=307.999849

x-request-id: d38e9425-4325-4939-a805-6181b1c162a9-1761303344

2025-10-24T10:55:44.183Z: Ensuring that the user is authenticated with the Partners API with the following scopes:



2025-10-24T10:55:44.183Z: Getting session store…
2025-10-24T10:55:44.185Z: Getting current session ID…
2025-10-24T10:55:44.186Z: Validating existing session against the scopes:
[
“openid”,
“https:// api.shopify .com/auth/shop.admin.graphql”,
“https:// api.shopify .com/auth/shop.admin.themes”,
“https:// api.shopify .com/auth/partners.collaborator-relationships.readonly”,
“https:// api.shopify .com/auth/shop.storefront-renderer.devtools”,
“https:// api.shopify .com/auth/partners.app.cli.access”,
“https:// api.shopify .com/auth/destinations.readonly”,
“https:// api.shopify .com/auth/organization.store-management”,
“https:// api.shopify .com/auth/organization.on-demand-user-access”,
“https:// api.shopify .com/auth/organization.apps.manage”
]
For applications:
{
“partnersApi”: {
“scopes”: 

}
}

2025-10-24T10:55:44.186Z: - Token validation → It’s expired: false
2025-10-24T10:55:44.188Z: Getting partner account info from cache
2025-10-24T10:55:44.230Z: Sending “Partners” GraphQL request:
query FindApp($apiKey: String!) {
app(apiKey: $apiKey) {
id
title
apiKey
organizationId
apiSecretKeys {
secret
}
appType
grantedScopes
applicationUrl
redirectUrlWhitelist
requestedAccessScopes
webhookApiVersion
embedded
posEmbedded
preferencesUrl
gdprWebhooks {
customerDeletionUrl
customerDataRequestUrl
shopDeletionUrl
}
appProxy {
subPath
subPathPrefix
url
}
developmentStorePreviewEnabled
disabledFlags
}
}

With variables:
{
“apiKey”: “*****”
}

With request headers:

User-Agent: Shopify CLI; v=3.86.1

Keep-Alive: timeout=30

Sec-CH-UA-PLATFORM: win32

Content-Type: application/json

to https:// partners.shopify .com/api/cli/graphql
2025-10-24T10:55:44.549Z: Request to https:// partners.shopify .com/api/cli/graphql completed in 318 ms
With response headers:

cache-control: max-age=0, private, must-revalidate

content-type: application/json; charset=utf-8

etag: W/“b1a4c0d269b1a9a93a32e8105871a637”

server-timing: processing;dur=64, socket_queue;dur=2.293, util;dur=0.1, cfRequestDuration;dur=200.999975

x-request-id: aa0f38da-4b2e-4c5f-ab1c-c1956e873dfa-1761303345

╭─ error ──────────────────────────────────────────────────────────────────────────────────╮
│                                                                                          │
│  No app with client ID 10300d228269d3c19b7a4a87f79af9b9 found                          │
│                                                                                          │
│  Next steps:                                                                             │
│    • Check that your account has permission to develop apps for this organization or     │
│      contact the owner of the organization to grant you permission                       │
│    • Run shopify auth logout to log into a different account than                      │
│      ---@gmail.com                                                                │
│    • Pass --reset to your command to create a new app                                  │
│                                                                                          │
╰──────────────────────────────────────────────────────────────────────────────────────────╯

2025-10-24T10:55:44.616Z: Running system process:
· Command: npm prefix
· Working directory: E:/Work_Web/Shopify/new_app/lean-vertical-app

2025-10-24T10:55:45.114Z: Obtaining the dependency manager in directory E:\Work_Web\Shopify\new_app\lean-vertical-app…
2025-10-24T10:55:45.927Z: Request to https:// monorail-edge.shopifysvc .com/v1/produce completed in 244 ms
With response headers:

x-request-id: 9f48cff1-261c-473d-8093-97b688927dcc

2025-10-24T10:55:45.927Z: Analytics event sent: {
“command”: “app dev”,
“time_start”: 1761303343008,
“time_end”: 1761303344573,
“total_time”: 1565,
“success”: false,
“cli_version”: “3.86.1”,
“ruby_version”: “”,
“node_version”: “25.0.0”,
“is_employee”: false,
“uname”: “windows amd64”,
“env_ci”: false,
“env_plugin_installed_any_custom”: false,
“env_plugin_installed_shopify”: “["
/cli"]”,
“env_shell”: “powershell”,
“env_device_id”: “b9097a169d2e32db2500375eb307183363fc8327”,
“env_cloud”: “localhost”,
“env_package_manager”: “npm”,
“env_is_global”: true,
“env_auth_method”: “device_auth”,
“env_is_wsl”: false,
“env_build_repository”: “Shopify/cli”,
“cmd_app_warning_api_key_deprecation_displayed”: true,
“cmd_app_all_configs_any”: true,
“cmd_app_all_configs_clients”: “{"shopify.app.toml":"d4f77e3a610e155de46dcf2149d4156b"}”,
“cmd_app_linked_config_used”: true,
“cmd_app_linked_config_name”: “shopify.app.toml”,
“cmd_app_linked_config_git_tracked”: true,
“cmd_app_linked_config_source”: “cached”,
“project_type”: “node”,
“app_extensions_any”: false,
“app_extensions_breakdown”: “{}”,
“app_extensions_count”: 0,
“app_extensions_custom_layout”: false,
“app_extensions_function_any”: false,
“app_extensions_function_count”: 0,
“app_extensions_theme_any”: false,
“app_extensions_theme_count”: 0,
“app_extensions_ui_any”: false,
“app_extensions_ui_count”: 0,
“app_name_hash”: “46f110994933dcfe67b048b460ef5b9f6e37fb61”,
“app_path_hash”: “ee1385f23a73baeac174b8538a11bd722860b91c”,
“app_scopes”: “["write_products"]”,
“app_web_backend_any”: true,
“app_web_backend_count”: 1,
“app_web_custom_layout”: true,
“app_web_framework”: “unknown”,
“app_web_frontend_any”: true,
“app_web_frontend_count”: 1,
“env_package_manager_workspaces”: true,
“cmd_all_timing_network_ms”: 720,
“cmd_all_timing_prompts_ms”: 0,
“cmd_all_launcher”: “unknown”,
“cmd_all_topic”: “app”,
“cmd_all_plugin”: “
/app”,
“cmd_all_verbose”: true,
“cmd_all_path_override”: true,
“cmd_all_path_override_hash”: “ee1385f23a73baeac174b8538a11bd722860b91c”,
“cmd_app_dependency_installation_skipped”: false,
“cmd_app_reset_used”: true,
“cmd_dev_tunnel_type”: “auto”,
“cmd_all_last_graphql_request_id”: “aa0f38da-4b2e-4c5f-ab1c-c1956e873dfa-1761303345”,
“cmd_all_timing_active_ms”: 844,
“cmd_all_exit”: “expected_error”,
“user_id”: “289710af-457e-4f4d-9ae8-92463fd46f99”,
“request_ids”: [
“d38e9425-4325-4939-a805-6181b1c162a9-1761303344”,
“aa0f38da-4b2e-4c5f-ab1c-c1956e873dfa-1761303345”
],
“args”: “–reset --verbose”,
“error_message”: “No app with client ID 10300d228269d3c19b7a4a87f79af9b9 found”,
“app_name”: “lean-vertical-app”,
“env_plugin_installed_all”: “["
/cli"]”,
“metadata”: “{"extraPublic":{},"extraSensitive":{}}”
}
2025-10-24T10:55:45.963Z: Reporting handled error to Bugsnag: No app with client ID 10300d228269d3c19b7a4a87f79af9b9 found
2025-10-24T10:55:46.023Z: Running system process:
· Command: npm prefix
· Working directory: E:/Work_Web/Shopify/new_app/lean-vertical-app

2025-10-24T10:55:46.513Z: Obtaining the dependency manager in directory E:\Work_Web\Shopify\new_app\lean-vertical-app…

Operating system

Windows 11

CLI version

3.86.1

Shell

PowerShell

Nodejs version

25.0.0

What language and version are you using in your application?

Node.js

Hi!

Looking at the warning about the `api-key`, it seems that you have a `SHOPIFY_API_KEY` environment variable defined, which is causing that error. Could you check that?

Thanks for the reply!
This is a newly created app using Shopify CLI, with no code or configuration changes made after initialization.
There’s no SHOPIFY_API_KEY or any other environment variable defined - everything is in its default state right after shopify app init.

That warning only appears when --api-key is passed or the SHOPIFY_API_KEY env var exists. And if it exists, that explains the error.

Could you run this in Powershell? $env:SHOPIFY_API_KEY

Another test: if you run shopify app dev --api-key wrong, you should see the same error, but with the ID wrong.

Finally, we will remove the support for that api-key flag in the next release. You can try it with the latest nightly, it should work for you: npm i -g @shopify/cli@nightly.