Exchange Control Panel (ECP) uses Outlook Web Access (OWA) logon UI to verify users. If you enable 2FA on OWA then ECP logon will be automatically secured by 2FA. 

However, if you want to enable MFA on ECP only but not on OWA, then please follow the guide below

Please note that it is not possible to enable MFA on OWA only but not on ECP.

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