A Microsoft app for iOS and Android devices that enables authentication with two-factor verification, phone sign-in, and code generation
Your tenant is currently in a mixed state because Authentication Methods migration is “Not Started.” This means Entra ID still considers both legacy authentication settings (such as per-user MFA and older SSPR configurations) and the modern Authentication Methods policy. The Microsoft script showing SMS/Voice disabled only reflects the modern policy - so users may still be using SMS because it remains enabled in the legacy configuration.
AFAIK, on September 1st, users with registered SMS or voice authentication methods should not automatically receive the passkey registration campaign if SMS/Voice is disabled in the modern Authentication Methods policy. However, leaving the tenant in the “Not Started” migration state creates risk because legacy methods may continue to function until Microsoft retires them. The larger impact occurs on February 1, 2027, when Microsoft retires Microsoft-managed SMS and voice delivery. Users who still depend on these methods may lose their ability to complete MFA or SSPR.
To avoid unexpected behavior, you should complete the migration to modern Authentication Methods. Change the migration state from Not Started to Migration Complete under Protection > Authentication methods > Manage migration so Entra ID uses only the modern policy. Also review the FIDO2/passkey settings and disable them if you do not want users registering passkeys, and set the Registration Campaign to Disabled instead of Microsoft-managed if you do not want Microsoft prompting users to register new methods.
For SSPR, requiring both Microsoft Authenticator and Email OTP can create registration issues. During the enforced combined security information registration process, users can immediately register Microsoft Authenticator, but Email OTP cannot normally be added during that sign-in interruption unless an email authentication method already exists. If users are required to register two methods and only have Authenticator available, they may be unable to complete registration and could be blocked.
A safer migration approach would be to first require only one SSPR method and have users register Microsoft Authenticator. After users have completed registration, instruct them to visit the My Sign-Ins (Security Info) portal to manually add Email OTP. Once most users have both methods registered, increase the SSPR requirement to two methods. Another option is to pre-register email authentication methods using Microsoft Graph, but this requires automation and additional validation because simply populating directory attributes such as alternate email does not automatically make the address a usable SSPR authentication method.
More at https://learn.microsoft.com/en-us/entra/identity/authentication/concept-sms-voice-retirement
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hth
Marcin