After his consecration in 1626, Ussher found himself in turbulent political times. Tension was rising between England and Spain, and to secure Ireland Charles I offered Irish Catholics a series of concessions, including religious toleration, known as the Graces, in exchange for money for the upkeep of the army. Ussher was a convinced Calvinist and viewed with dismay the possibility that people he regarded as anti-Christian papists might achieve any sort of power. He called a secret meeting of the Irish bishops in his house in November of 1626, the result being the "Judgement of the Arch-Bishops and Bishops of Ireland". This begins:
The religion of the papists is superstitious and idolatrous; their faith and doctrine erroneous and heretical; their church in respect of both, apostatical; to give them therefore a toleration, or to consent that they may freely exercise their religion, and profess their faith and doctrine, is a grievous sin.
The Judgement was not published until it was read out at the end of a series of sermons against the Graces given at Dublin in April 1627. In the end, the Graces were not confirmed by the Irish parliament.
During a four-year interregnum between Lord Deputies from 1629 on, there was an increase in efforts to impose religious conformity on Ireland. In 1633, Ussher wrote to the new Archbishop of Canterbury, William Laud, in an effort to gain support for the imposition of recusancy fines on Irish Catholics. Thomas Wentworth, who arrived as the new Lord Deputy in Ireland in 1633, deflected the pressure for conformity by stating that firstly, the Church of Ireland itself would have to be properly resourced, and he set about its re-endowment. He also settled the long-running primacy dispute between the sees of Armagh and Dublin in Armagh's favour.
Ussher soon found himself at odds with the rise of Arminianism and Wentworth and Laud's desire for conformity between the Church of England and the more Calvinistic Church of Ireland. Ussher resisted this pressure at a convocation in 1634, ensuring that the English Articles of Religion were adopted as well as the Irish articles, not instead of them, and that the Irish canons had to be redrafted based on the English ones rather than replaced by them. Theologically, he was a Calvinist although on the matter of the atonement he was (somewhat privately) a hypothetical universalist. His most significant influence in this regard was John Davenant, later an English delegate to the Synod of Dort, who managed to significantly soften that Synod's teaching regarding limited atonement.
In 1633 Ussher had supported the appointment of Archbishop Laud as Chancellor of Trinity. He had hoped that Laud would help to impose order on what was, Ussher accepted, a somewhat mismanaged institution. Laud did that, rewriting the charter and statutes to limit the authority of the fellows, and ensure that the appointment of the provost was under royal control. But he also in 1634 imposed on the College an Arminian provost, William Chappell, whose theological views, and peremptory style of government, were antithetical to all that Ussher stood for. By 1635, it was apparent that Ussher had lost de facto control of the church to John Bramhall, Bishop of Derry, in everyday matters, and to Laud in matters of policy.
The traditional view of Ussher is of a slightly-unworldly scholar, who was, at best, a mediocre politician and administrator. In reality he was an effective bishop and archbishop, and politically important; however, he was reactive and sought conciliation rather than confrontation. The story that he successfully opposed attempts to reintroduce the Irish language for use in church services by William Bedell, the Bishop of Kilmore, has been refuted .
Ussher certainly preferred to be a scholar when he could be. He engaged in extensive disputations with Roman Catholic theologians, and even as a student he challenged a Jesuit relative, Henry Fitzsimon (Ussher's mother was Catholic), to dispute publicly the identification of the Pope with the Antichrist. However, Ussher also wrote extensively on theology, patristics and ecclesiastical history, and these subjects gradually displaced his anti-Catholic work. As well as by his learning, he was also distinguished by his charity and good temper.
After Convocation in 1634, Ussher left Dublin for his episcopal residence at Drogheda, where he concentrated on his archdiocese and his research. In 1631, he had published a
Discourse on the Religion Anciently Professed by the Irish, a ground-breaking study of the early Irish church, which sought to demonstrate how it differed from Rome and was, instead, much closer to the later Protestant church. This was to prove highly influential, establishing the idea that the Church of Ireland was the true successor of the early Celtic church - a belief which persists down to the present day.
In 1639, he published the most substantial history of Christianity in Britain to that date,
Britannicarum ecclesiarum antiquitates - the antiquities of the British churches. It was an astonishing achievement in one respect - in gathering together so many previously unpublished manuscript sources. But Ussher was very reluctant to arrive at firm judgements as to the sources' authenticity - hence his devotion of a whole chapter to the imaginative but invented stories of King Lucius and the creation of a Christian episcopate in Britain.
