Firstly, you need to have Lumia Administrator permissions to deactivate an account in the organisation.
From the Configuration cog, select "Manage People"
Find the employee for whom you wish to deactivate, and click the hamburger menu on the right-hand side of the screen:
The following message will appear. Check the confirmation box and select “Deactivate account" to finalise this step.
What happens next?
The employee will show as inactive in the people directory and will no longer have access to Lumia:
Converting between Stakeholders and Employees