DUO with Office 365

We are using DUO 2FA to secure our users Exchange Online, but this has now caused us a problem with one of our applications.
We are using an online call logging system that accesses a user mailbox in Office 365 to send and import new emails, but since we have implemented DUO this has stopped working.
Does anyone know if there is any way round this?
I know this is fairly vague, but i am not sure what information you would need.

I’d recommend looking into the Azure AD Conditional Access to protect your O365 users.
That way you can protect a all users in a group, and can exclude the mailbox that the call logging system is working with.

The other thing worth checking is if the Call Logging System is using Basic Auth (e.g. IMAP) or if they can be setup using OAuth.
Microsoft have announced that they are deprecating Basic Auth, so it may brake soon anyway regardless of the Duo side.

There is probably an App Registration set-up in Azure AD for your call logging system.

You may need to exclude this application from the Conditional Access policy which is applying the Duo MFA custom control.