Migrating from one on-premise Exchange to multiple Office 365 instances

If you currently have users from multiple organizations (separate e-mail domain names) within a single on-premise Exchange server, you may consider splitting them into their own self-contained instances of Office 365.  This will provide each organization with better confidentiality and control over their internal data without any direct additional cost (since Office 365 is licensed per user anyway).

Microsoft provided some guidance on how to do this in the Office 365 Community Article: Migrating onsite Exchange to two different Office 365 plans.  While this example show two different plans, it could be two (or more) instances of the same plan as well.

The downside of this approach is that users from the organizations will lose the direct/internal collaboration features (e.g. seeing free/busy schedule of users from the other organization) that they may be used to using.

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