Office 365 user accounts can be manually deleted by using the:
- Office 365 portal.
- Microsoft Online Services Module for Windows PowerShell (or a script)
- Microsoft Exchange Online Exchange Control Panel.(ECP)
Furthermore user accounts can be deleted through a synchronized deletion:
- if directory synchronization filtering changes exclude the on-premises Active Directory user object from the synchronization set. (Directory synchronization filtering changes are also known as scoping.)
- if the on-premises user object was deleted from on-premises Active Directory schema.
If one of your user account was accidentally deleted from Office 365 it can still be restored. A deleted user object isn't immediately and completely removed from Microsoft Online Directory Service. The user object is put in a deleted state (sometimes refered to as a 'Soft Delete') and no longer appears in the ordinary user listing. However, it's present in the Microsoft Online Directory Service database and can be recovered for a tenant within 30 days.
To determine whether a user object is still eligible to be recovered from a deleted state, and possible resolutions, follow the steps in this article from Microsoft Support.