There are two versions of the powershell module that you use to connect to office 365 and administer user accounts groups and licenses mfa run one of these commands from a windows powershell command prompt run the install module msonline command if prompted to install the nuget provider . Connect to office 365 services with multifactor authentication mfa and powershell . You need to use separate sessions of the exchange online remote powershell module o delegated access permission dap partners cant use the procedures in this topic to connect to their customer tenant organizations in exchange online powershell mfa and the exchange online remote powershell module dont work with delegated authentication. Connect with mfa to exchange online by patrick lamber on feb 3 2017 filed under security governance best practices office 365 exchange online. To save everyone from having to read anna chu full post there is now an exchange online powershell module in preview available that supports mfa i just tested it and it works so far as expected authenticating to o365 using powershell and mfa you cant that cmdlets method was created years before mfa was even a thing
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