How to delete directory synced users from the Office 365 dashboard

To be able to delete directory synced users on Office 365 dashboard, you have to disable the sync first on your on-premise server:

1. Open Azure Active Directory Module for Windows PowerShell

2. Connect to the Office 365 server by running this cmdlet in PowerShell and enter your Office 365 admin user (e.g. yyy@xxxx.onmicrosoft.com):

Connect-MsolService

3. Run this following command to disable directory sync:

Set-MsolDirSyncEnabled –EnableDirSync $false

It may take to 72 hours for the deactivation fully done.

4. Check if the sync was fully disabled by this command:

(Get-MSOLCompanyInformation).DirectorySynchronizationEnabled

5. Go Office 365 dashboard and delete the users you want


Reference: https://support.microsoft.com/en-gb/kb/2619062