MFA & Verification Issues

Fix Only Microsoft Authenticator Appearing for MFA Setup

Jason Miller Oct 21, 2026 869 views

Question details

Users are restricted to using the Microsoft Authenticator app during MFA setup, despite SMS and phone methods being enabled in the portal.

How to Fix Only Microsoft Authenticator Appearing for MFA Setup

Product: Microsoft 365 / Microsoft Entra ID
Device & OS: not provided
Scenario: A new user is attempting to set up multifactor authentication for the first time.
Observed behavior: Only the Microsoft Authenticator app is displayed as an option for setup, while SMS and phone authentication options are completely missing.

Before you start

Ensure you have Global Administrator or Authentication Policy Administrator privileges in the Microsoft Entra admin center before modifying authentication methods.

Solution 1Recommended

Check Microsoft Entra Authentication Methods Policy

Verify that the specific SMS and Phone methods are properly enabled and targeted to the affected users in the Entra ID authentication methods policy.

Microsoft 365 is transitioning from legacy MFA portals to the centralized Entra ID Authentication Methods policy. Settings configured in the old portal may not apply if the new policies are overriding them.

Access the Admin Center

Navigate to Authentication Methods

In the left-hand navigation menu, go to Protection, then select Authentication methods, and click on Policies.

Enable SMS Authentication

Select the 'SMS' method from the list. Ensure the toggle is set to 'Enable' and that the Target is set to 'All users' or the specific group of affected users.

Enable Voice Call Authentication

Go back to the Policies list, select 'Voice call', and verify that it is also enabled and correctly assigned.

Check Microsoft Entra Authentication Methods Policy

Policy Application Time: It may take up to 15 minutes for new authentication policy changes to propagate and become visible to users during their MFA setup.

Solution 2

Review Registration Campaign Settings

Check if a Microsoft Authenticator registration campaign is forcing users to default to the app over other methods.

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Frequently Asked Questions

Why is SMS missing from the MFA setup page even though it is enabled in legacy MFA settings?

Microsoft is migrating authentication methods management entirely to the Entra ID Authentication Methods policy. Settings enabled in the legacy multi-factor authentication portal might be ignored if the migration to the new policy framework is active for your tenant.

Can I permanently force users to use Microsoft Authenticator instead of SMS?

Yes. By utilizing the Registration Campaign feature in Microsoft Entra ID, you can prompt or require users to set up the Authenticator app as their primary MFA method, which is highly recommended by Microsoft to prevent SMS interception attacks.

What should I do if the Entra policies are correct but the issue persists?

If both your Authentication Methods policies and registration campaigns are configured correctly and SMS still does not appear in the setup wizard, you should contact Microsoft 365 support to investigate potential backend synchronization delays or tenant-level glitches.

Login & Account Issues