Set up a different authentication app link does nothing, forced to use Microsoft Authenticator

The Cyber Friend 0 Reputation points
2026-11-04T13:33:26.41+00:00

I’m the admin on our Microsoft 365 tenant and I’m stuck trying to set up MFA on one of our accounts. When I sign in as the user, I get the “Let’s keep your account secure” screen that forces me to install Microsoft Authenticator. The link that says “Set up a different authentication app” doesn’t do anything when I click it, and I only get one choice, which is Microsoft.

I use Keeper for the MFA codes on all my other accounts, so I’d like to use it here too. I tried entering the secret key manually into Keeper, copy and pasted so there was no typo, but the six digit codes were never accepted.

Here is what I’ve already checked and tried:

  1. In Entra under Authentication methods, Software OATH tokens is enabled for All users. Microsoft Authenticator, Temporary Access Pass, Password and Email OTP are also enabled.
  2. I tried two different browsers.
  3. I created a Temporary Access Pass and used it to get to the Security info page. When I click Add sign in method, the only option listed is Microsoft Authenticator. Clicking through that flow still doesn’t give me a working option for a different authenticator app.

Has anyone run into this when Software OATH tokens is already turned on? Is there a setting I’m missing that makes the “different authenticator app” option show up, or is this a known problem right now? I’d really like to avoid being forced onto the Microsoft app for this one account.

I also want to note, we can still add the secret key to Keeper and it gives us a 6 digit code, but Microsoft rejects the code every time. Four other users in our environment use Keeper for their 2FA and theirs works fine, so third party apps do work in our tenant. It’s only this one account that has the problem.

Thanks in advance for any help.

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  1. Dora-T 2,075 Reputation points Independent Advisor
    2026-11-05T05:46:28.35+00:00

    Hi @The Cyber Friend

    I tested this behavior in my own test tenant with Software OATH tokens enabled and was unable to reproduce the issue.

    I tested with a newly created account and, after selecting "Set up a different authentication app", the registration flow proceeded normally and displayed the QR code for a third-party authenticator app. I was then able to complete the registration successfully using the generated verification code.

    I also tested through My Sign-Ins > Add sign-in method > Microsoft Authenticator > Set up a different authentication app, and the option worked as expected in my environment.

    User's image

    In the meantime, please check whether any Conditional Access policies are applied specifically to the affected account and differ from the users who are able to use Keeper successfully.

    If the affected account is configured the same way as the other users' accounts and the issue persists, I recommend submitting a support request through the Microsoft 365 Admin Center so Microsoft Support can investigate further.

    For instructions, please refer to: Get support - Microsoft 365 admin | Microsoft Learn.    

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