@Ben Mac
Currently we are 100% O365 mailboxes this on-prem will not host any mailboxes
Are those mailboxes created on Exchange online? If so, it will be an expected behavior that cannot see those Office 365 mailboxes from Exchange on-premises EAC.
For Exchange on-premises EAC, you can only see mailboxes which AD account hosted on local AD. Such as:
- Exchange on-premises mailbox created in Exchange on-premises, then migrated to Exchange online later.
- Office 365 type mailbox which created from Exchange on-premises EAC.
Those two kind mailboxes‘ AD account are all hosted on local AD and sync with AAD.
So, if you want to from Exchange on-premises manage Office 365 mailboxes which created on Exchange online, you need to create local AD account for those mailbox, then match local AD account with AAD account.
For more detailed information, you can have a look about this article: https://www.codetwo.com/admins-blog/how-to-merge-an-office-365-account-with-an-on-premises-ad-account-after-hybrid-configuration/#no-local-account
Please Note: Since the web site is not hosted by Microsoft, the link may change without notice. Microsoft does not guarantee the accuracy of this information.
If the response is helpful, please click "Accept Answer" and upvote it.
Note: Please follow the steps in our documentation to enable e-mail notifications if you want to receive the related email notification for this thread.