Hello @L.Han,
Thank you for posting your query on Microsoft Q&A.
Based on your description, I understand that you have enabled Microsoft Authenticator and SMS authentication methods for your user account but are experiencing issues with SMS. In the modern authentication methods, SMS is enabled for all users, while Microsoft Authenticator is disabled.
Given this setup, only SMS authentication should work. If a user tries to sign in using Microsoft Authenticator, it should not be accepted since it’s disabled in your settings. However, this behavior can be overridden if legacy verification options or legacy authentication methods are still enabled in your tenant, and the migration to modern methods is incomplete.
Please refer to the screenshot below to check the migration status.
If the migration is marked as completed, only methods from the Modern Authentication Methods policy will be applied. If the status is "in progress" or "pre-migration," legacy verification options may still be used during authentication. You can find these settings under Microsoft Entra ID > Users > Per-User MFA > Service settings > Methods available to users.
Check which methods are enabled in your tenant and troubleshoot accordingly. If you still encounter issues, please let me know, and we can connect offline for further assistance.
I hope this information is helpful. Please feel free to reach out if you have any further questions.
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Thanks,
Raja Pothuraju.