In order for Office desktop clients, such as Outlook, Skype for Business, to support MFA via federated authentication, your Office 365 tenant needs to be configured to support modern authentication.
Finally, import the new session into the Windows PowerShell console.
Import-PSSession $session
Run the following command to enable modern authentication: Set-CsOAuthConfiguration -ClientAdalAuthOverride Allowed
Verify that the change was successful by running the following: Get-CsOAuthConfiguration
Note: to disable modern authentication, run command: Set-CsOAuthConfiguration -ClientAdalAuthOverride NoOverride
However, not all Office desktop clients support modern authentication. Generally speaking, Office 2013 and later desktop clients (including Outlook and Skype for Business) support modern authentication. Check the link below for the list of Office clients that support modern authentication: