For more information about GitHub App manager permissions, see "Permission levels for an organization."
Removing a GitHub App manager's permissions for the entire organization
- In the top right corner of GitHub Enterprise Server, click your profile photo, then click Your organizations.

 - Next to the organization, click Settings.

 - In the left sidebar, click GitHub Apps.

 - Under "Management", find the username of the person you want to remove GitHub App manager permissions from, and click Revoke.

 
Removing a GitHub App manager's permissions for an individual GitHub App
- In the top right corner of GitHub Enterprise Server, click your profile photo, then click Your organizations.

 - Next to the organization, click Settings.

 - In the left sidebar, click GitHub Apps.

 - Under "GitHub Apps", click on the avatar of the app you'd like to remove a GitHub App manager from.

 - In the left sidebar, click App managers.

 - Under "App managers", find the username of the person you want to remove GitHub App manager permissions from, and click Revoke.
