With multi-domain Exchange 2013 mail server, we need to:
- Create a certificate with the primary domain that contains at least:
- Launch the migration wizard and complete it
- On IIS add bindings for the default web site where the autodiscover app is located
- Add an autodiscover binding for all your domains, like autodiscover.mysecondarydomain.xyz, autodiscover.myprimarydomain.xyz, *.myprimarydomain.xyz with 443 port and the correct certificate. Be sure to make the tick on Require Server Name Indication.