Is it safe to delete Entra registered devices when they are already Entra joined?

yep - it's generally safe to remove the old Entra registered device objects after the devices have been successfully onboarded to Intune and are now Entra joined, but there are a few things you should verify first before deleting them. In most cases, the duplicate “Entra registered” records are remnants of the previous registration state and are no longer actively used once the device has been properly Entra joined and managed by Intune.

Before deleting anything, confirm that the Entra joined device is the active object. The active device should show as compliant in Intune, have recent sign-in activity, and appear as “Microsoft Entra joined” rather than “Microsoft Entra registered.” You should also confirm that Conditional Access policies, compliance policies, and application access are evaluating against the new joined device object and not the old registered one.

One important consideration is whether users were previously using the registered device object for authentication methods tied to device identity, such as Conditional Access policies requiring a registered or compliant device. If the Entra joined device is healthy and reporting correctly, users should continue to have access without interruption after the old registered object is removed. However, if the joined device has not fully completed enrollment, compliance evaluation, or hybrid identity synchronization, deleting the old object too early could temporarily affect access to applications protected by Conditional Access.

You should also check whether any BitLocker recovery keys, local admin assignments, endpoint security policies, or application targeting are associated with the old registered object. Normally these settings move to or are recreated under the new Intune-managed Entra joined device, but it is worth validating before cleanup. If BitLocker keys are involved, verify they exist on the active device record in Entra ID or Intune before removing the older object.

Deleting the stale Entra registered device objects does not uninstall Intune management, remove the device from the user, or wipe the computer. It only removes the obsolete identity record from Entra ID. The active Entra joined and Intune-managed device object remains unaffected as long as you delete the correct object.

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hth

Marcin