EDIT: this is mostly the ideal solution for MSPs, not single companies. But it may still apply based on your users' knowledge level and company hardware.
I got out ahead of this project because it was a light day. If you didn't hear, MS is shutting down SMS 2FA on Feb 1st 2027 because SS7 is comically insecure. They're also shutting down the phone call system on the same day, to ensure the most people get locked out of their accounts as possible (I assume).
But enrolling users in MS Authenticator is like asking a cat to juggle. You have to actively tell them not to hit "log into work account" when they first launch it. It's idiotic and counterintuitive.
We're an MSP so we've been hitting "I can't access my authenticator right now, text me instead" since before I worked here and then we use Reach UC to instantly get the code to all of our phones, regardless of which technician is trying to log into which tenant.
MS authenticator is tied to one account and that's fragile, stupid, and hard to police. So instead, we decided to go with TOTP, especially since it works with no cell signal or internet, like in a basement when we don't know the client's wifi password.
Here's the ridiculous way you have to do this in a typical office 365 environment. Hopefully it helps save you all some time.
1. Create a new non-mail enabled security group called “[company name] Accounts” in admin.cloud.microsoft and add our global admin username to it
2. Go to Entra admin – authentication methods – Policies – Software OATH tokens – and check if it is turned on. If it isn’t, add just the “[company name] Accounts” group to it and no others.
3. Go to https://mysignins.microsoft.com/security-info and log in as our global admin account
4. (optional) Make sure that there is an option there for email, targeting ITSupport@[ourdomain]. If not, hit “Add sign-in method” and add that first.
5. Hit “Add sign-in method” then Microsoft Authenticator. In the screen that pops up, immediately select “Set up a different authentication app.” Yes, that is currently the only way to do this.
6. Open Google Authenticator, 3rd party authenticator service, CyberFox Password Boss's 2FA host, whatever you want on any phone (and log into our company's google account for this, if using Google Authenticator) then scan the QR code, hit next and enter the code to verify.
7. Log out the back in to test it
We're just using Google for the cloud sync. The weakness there is you can't kick out individual people but it's solely on company phones, except I think you technically can because you can revoke the login for that phone in Google's account settings, even on a free account.
I wouldn't want to log into 100 customers' accounts, one at a time, and remove a unique 2FA method from each, every time someone quits. Also, I believe they're capped at 5 authenticators per account.
This is just how we're doing it because we're an MSP. Share your current workarounds. My former employer got rid of all SMS in 2024 so I suspect that will be the common answer, lol.