The key to a successful MFA deployment starts by enabling modern authentication. Modern authentication brings Active Directory Authentication Library (ADAL)-based sign in to your Office 365 applications, and without this enabled, end users will have to use “App Passwords”, witch is a true nightmare for any user and it department.
By default Office 365 tenants (Exchange Online, SharePoint Online and Skype for Business Online) will need to be configured to accept a modern authentication connection. I recommend that you enabled for modern authentication both Exchange Online and Skype for Business, if you want to use MFA.
This Script will guide you through the process of enabling modern authentication for Skype for Business Online.