In 1626, having migrated to Ireland, Bernard was ordained by Archbishop James Ussher, Archbishop of Armagh from 1625 to 1656, in St. Peter's church, Drogheda. He became Ussher's chaplain and librarian. In 1627 he became Dean of Kilmore, a titular position. He was incorporated at Oxford in 1628 as well as becoming the Rector of St. Peter, Drogheda. In 1637 he exchanged with Henry Jones the deanery of Kilmore for that of Ardagh, making him the Dean of Ardagh, he also became prebendary of Dromore. He continued to be the dean until 1641, when he had to flee to England during the rebellion.