Click the user menu (your icon) > Organization Settings.
Click the Tokens tab.
Click Edit next to the agent token you'd like to change.
The permissions dialog allows you to edit a token's ability to access certain deployments. By default, agent tokens have permission to access any deployment in the organization including branch deployments. This is called Org Agent and is set using the toggle in the top right of the dialog. To edit individual deployment permissions, Org Agent has to first be toggled off.