I'm doing a migration of a client this week and each day getting several users setup on it....for Teams, OneDrive, etc. Retiring their old on-prem server. Moving to "The Cloud"
I have clients download the Microsoft Authenticator app...ahead of time. Send out an email explaining how to do so. Saves you time on the phone, there's always a few users that have an iphone and don't know their Apple ID which is required to install from the iTunes store...so you don't want to deal with that time waster while on the phone.
Once they have that installed, you can then schedule your remote session.
Once I'm doing the phone/remote session with them, I have their 365 tenant open on my computer, I enable MFA on their account.
I remote into their computer....I then open office.com on their computers browser....username....password....and then the expected "Additional information is required" dialog box kicks in.
I prefer the "Approve/Deny" method via the Authenticator app...so I select the radio button and download menu choices for Auth app and send request to phone.
I have the user open the app, skip the backup stuff, go to add account, Work/School out of the 3 choices, allow app to access camera....hold camera up, I click next...have them grab the QR code, send the test..they approve...and then fill in the cell phone number in the next screen as the alternate method for the old fashioned text code to phone approach.
On their computer, log out of office.com, log in...test...show them the ropes.
Now close any Office apps...and open...I usually pick Word first...I have them log out of Word (if 365 sourced)...log in...username, password..approve MFA. It will also ask to manage computer, have a check in the box. Same with Teams, same with OneDrive. OneDrive sometimes slower....sometimes a reboot of the rig to settle OneDrive in.
Some computers won't adjust to it...so clear the apps logins in Credential Manager...and run through the logins again.
Now, when you're at the office.com as Admin....and you see the list of users...there's the "Manage Multifactor" box along the top. If not there...hit "refresh" when you're at the top of the users list.
I'm wanting to find out more info...but this is a "basic" MFA control. Somehow different from the MFA control when you're over in Azure Admin. You can have one say "enabled" and the other say "disabled"...and it'll be enabled.
I'm "guessing" that when you enable MFA on the Azure admin side....it allows the control within "conditional access". Such as...never ask for MFA when the request comes from <WAN IP of clients office>. Or from Azure managed devices (you know that "allow this device to be managed checkbox when you put a check in at the app sign in?"