Ellys continued to hold his prebend and his city living in commendam, and went every Sunday morning i winter from his house in Queen Square to preach to his parishioners.
He complained that Cashel was only worth £98 and – in spite of the misgivings of William Cecil, Lord Burghley – was granted the See of Waterford and Lismore in commendam, which he held until 1589, and then again from 1592 upon the death of Bishop Wetherhead.
Thomas was never bishop of Dunkeld in anything but name, so had no revenue, although King James did make him Abbot of Coupar Angus in commendam.