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
After running this command:
shopify app init
with npm as the system’s only package manager. Then it should not create the pnpm-workspace.yaml file.
Actual behavior
It is created the pnpm-workspace.yaml file.
Reproduction steps
shopify app init
Verbose output
2026-08-24T08:57:20.735Z: Running command app init
2026-08-24T08:57:20.781Z: Ensuring that the user is authenticated with the App Management API with the following scopes:
2026-08-24T08:57:20.782Z: Getting session store…
2026-08-24T08:57:20.786Z: Getting current session ID…
2026-08-24T08:57:20.788Z: Validating existing session against the scopes:
[
“openid”,
cannot put links
]
For applications:
{
“appManagementApi”: {
“scopes”:
},
“businessPlatformApi”: {
“scopes”:
}
}
2026-08-24T08:57:20.789Z: - Token validation → It’s expired: false
2026-08-24T08:57:20.792Z: 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=4.7.0
- Keep-Alive: timeout=30
- Sec-CH-UA-PLATFORM: win32
- Content-Type: application/json
to https://destinations.shopifysvc.com/destinations/api/2020-07/graphql
(… …)
╭─ info ───────────────────────────────────────────────────────────────────────╮
│ │
│ Initializing project with npm │
│ Use the --package-manager flag to select a different package manager. │
│ │
╰──────────────────────────────────────────────────────────────────────────────╯
Installing dependencies with npm …
Operating system
Windows 10
CLI version
4.7.0