Hello Sean O'Brien,
Thanks for your patience while we checked this. We were able to reproduce the same behavior, and what you’re seeing is expected.
When connecting to a VM from the Azure portal using Azure Bastion, the Microsoft Entra ID login option is shown only if the signed-in user has one of the following built-in roles:
Virtual Machine Administrator Login
Virtual Machine User Login
If those roles are removed and only a custom role is assigned, even with the same login permissions, the Entra ID option no longer appears. The Bastion experience in the portal checks for these specific built-in roles, not just the underlying permissions.
This applies only to the Azure portal + Bastion UI and matches the current Entra ID authentication for Bastion (Preview) behavior. The requirement for these built-in roles is clearly listed in the Prerequisites section of the documentation.
Entra ID login with custom roles still works when using native RDP or Bastion via CLI.
Workaround:
To use Entra ID authentication from the Azure portal with Bastion, assign Virtual Machine Administrator Login or Virtual Machine User Login. Custom roles aren’t supported for this portal flow at the moment.
References