Dear bmc,
Thank you for the details. Since the same YubiKey is still working for accounts that were enrolled two weeks ago, it suggests the key itself is functioning correctly. To help narrow this down, could you please check the following?
- Did there any error message appear when the 6-digit code is rejected?
- If you review the user's Sign-in logs, what is the failure reason shown for the failed MFA attempt? For reference: What are Microsoft Entra sign-in logs?
In the meantime, if the YubiKey was enrolled by an administrator on behalf of the user, please first verify that the hardware OATH token has been successfully activated in Microsoft Entra ID.
You can check this by signing in to the Microsoft Entra admin center, navigating to Entra ID > Multifactor authentication > OATH tokens, and confirming that the token status shows as Activated. If the token is listed but not activated, the generated 6-digit codes will not work for authentication.
For more information, you can refer to this article: Using YubiKeys with Microsoft Entra ID MFA OATH-TOTP
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