An error occurred while saving the commentAdam Cloud commented
There are workarounds to get this to work but it would be nice if there was an easy way to do this.
Since this is probably low priority, what i did is i had to make it so that an account that is admin for the Azure Active Directory was also admin on the subscription.
I then went to the old portal (manage.windowsazure.com) and changed the directory of the subscription to use the azure active directory.
You can then add your MSA account back as a guest to the directory and then you should be able to log into either and have access.