After deleting all required objects from Azure AD, so you could delete it, the “Delete directory” validator still says “Delete all enterprise applications”, as there are custom Enterprise Applications preventing directory deletion.
Usually the reason is Microsoft Visual Studio Team Services Enterprise application. You can go to Properties, and flip “Enable for users to sign-in” to No, and it helps in some cases.
However, sometimes it is not enough, but you need to go and delete all Enterprise Applications via PowerShell (although many of them are internal Azure apps).
Command for logging in and deletion is:
Connect-AzureAD –TenantID <TENANT_ID>
#repeat the following line for EACH Enterprise Application, some will throw error, but ignore it
Remove-AzureADServicePrincipal –ObjectId <OBJECT_ID_OF_ENT_APP>
Then with your web browser, log out from the Azure portal, and log back in, and you should be able to delete the Azure AD using browser.
Do note that Get-AzureADServicePrincipal | Remove-AzureADServicePrincipal didn’t work for some reason, and I needed to do the removal one by one.