About base permissions for an organization
You can set base permissions that apply to all members of an organization when accessing any of the organization's repositories. Base permissions do not apply to outside collaborators.
If someone with admin access to an organization's repository grants a member a higher level of access for the repository, the higher level of access overrides the base permission.
Setting base permissions
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 Member privileges.
Under "Base permissions", use the drop-down to select new base permissions.
Review the changes. To confirm, click Change default permission to PERMISSION.