Per-user MFA is still supported and will continue working just fine after September. Not sure where you are getting your info, but Microsoft has NOT announced deprecation of per-user MFA yet.
Microsoft 365 and Legacy MFA
We have Microsoft 365 E1 and E3 licenses. We also have a hybrid environment with active directory hosted internally. We use Azure AD Connect to sync with Microsoft 365 and a federation server to log users into their Microsoft 365 accounts. We also have per-user MFA set up through Microsoft 365, not Security Defaults. We were told Microsoft will no longer support this after September 30, 2024.
We do not have a Microsoft premium license (P1, P2, etc) so we cannot set up any kind of conditional access.
What can I do to resolve this? Is the only alternative to enable Security Defaults? What happens to all of our service accounts if I do this? If I enable Security Defaults, will all users need to set it up again?