You can add exceptions/whitelist to your CA policy to address those scenarios. Or you can wait for Microsoft to release a solution, as they have promised in the latest blog posts.
conditional access block legacy authentication onprem powershell scripts

Hello all
We have a number of powershell scripts that are running onprem that run via a scheduled task. The scripts log into Exchange online and SharePoint online and perform many functions. If we block legacy access into the tenant, this will prevent the scripts from being able to log in. I know we can configure powershell to use MFA, however its not realistic or practical to have a user repsond to the mfa challenge, as these scripts are running off hours. How do we get around this? We want to block legacy access but we dont want our scripts to stop working
Thank you
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skip hofmann 46 Reputation points
2020-04-26T18:39:28.033+00:00 Can you point me to that blog post you are referring to ?