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Hi Bindu M S
Based on my research regarding the [External] tag remaining visible for Multi-Tenant Organization (MTO) members using your custom domain. This behavior arises from how the automated MTO configuration wizard interacts with Exchange Online’s mail flow boundaries
When the setting “Suppress Outlook external tag for MTO members” is enabled, Microsoft 365 automatically creates a backend Remote Domain entry for the partner tenant and marks it as internal (IsInternal = $true). This specific flag is what instructs Outlook to suppress the external tag.
However, the automated MTO setup wizard only provisions this Remote Domain for the partner tenant's default routing domain (.onmicrosoft.com). It does not automatically discover or add custom vanity domains (like @contoso.com).
Because of this:
- Messages via
@contoso.onmicrosoft.commatch the automated entry > recognized as internal > Tag is suppressed. - Messages via
@contoso.comfail to match the entry > classified as standard inbound mail > Tag is displayed.
This also explains why the issue is strictly bidirectional and why standard cross-tenant services like Teams work perfectly (as Teams relies on Entra ID cross-tenant sync attributes, whereas Outlook strictly follows Exchange mail flow perimeters).
The Set-ExternalInOutlook -AllowList cmdlet evaluates the visible From address (P2 sender). In complex MTO setups, Outlook’s perimeter logic defers heavily to defined Remote Domains. If a domain isn't explicitly classified as an internal mail flow boundary via a Remote Domain entry, standard allowlist overrides are frequently bypassed.
To resolve this, you will need to manually define the custom domain as an internal Remote Domain boundary. Because this affects inbound mail flow, these steps must be completed by an Exchange Administrator in both tenants for each other's custom domains.
Note: The option to mark a Remote Domain as internal is not exposed in the Exchange Admin Center (EAC) visual interface. You must create the domain via the admin portal and then flip the internal flag using PowerShell
Create the Remote Domain in the Portal
- Open the Exchange Admin Center (admin.exchange.microsoft.com).
- Navigate to Mail Flow > Remote Domains and click *Add a remote domain > *Name it descriptively (for example:
MTO Partner Vanity Domain). - In the Domain box, type the partner's custom domain (ex:
contoso.com) > Click Save.
Set the Domain to Internal via PowerShell
Connect to Exchange Online PowerShell:
Connect-ExchangeOnline
Run the following command using the exact name you specified in step "Create the Remote Domain in the Portal"
Set-RemoteDomain -Identity "MTO Partner Vanity Domain" -IsInternal $true
Allow Time for Replication
Exchange Online mail-flow perimeters and Outlook configuration tables rely on heavy client-side and cloud caching. Please allow 24 to 48 hours for these changes to fully replicate across all Outlook endpoints (Desktop, Web, and Mobile).
Since manually creating Remote Domains introduces extra management overhead whenever you add new custom domains in the future, you may want to open a formal support ticket with official Microsoft 365 Support. This helps bring visibility to the limitation so the Microsoft product team can consider expanding the MTO wizard's automated domain scope in future updates.
I hope this information helps and if you have any further question, please feel free to let me know via comment section!
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