Calls made by service principals aren't blocked by Conditional Access.

Service accounts like these should be excluded since MFA can't be completed programmatically. They're normally used by back-end services allowing programmatic access to applications, but are also used to sign in to systems for administrative purposes. Service accounts are non-interactive accounts that aren't tied to any particular user.

Service accounts and service principals, such as the Azure AD Connect Sync Account.

More information can be found in the article, Manage emergency access accounts in Azure AD.

In the unlikely scenario all administrators are locked out of your tenant, your emergency-access administrative account can be used to log into the tenant to take steps to recover access. Emergency access or break-glass accounts to prevent tenant-wide account lockout.User exclusionsĬonditional Access policies are powerful tools, we recommend excluding the following accounts from your policies: The guidance in this article will help your organization create an MFA policy for your environment. Your password doesn't matter, but MFA does! Based on our studies, your account is more than 99.9% less likely to be compromised if you use MFA. As Alex Weinert, the Directory of Identity Security at Microsoft, mentions in his blog post Your Pa$$word doesn't matter:

Microsoft 365 mfa setup