He became Professor of Theological Controversies at Trinity College and a Bachelor of Divinity in 1607, Doctor of Divinity in 1612, and then Vice-Chancellor in 1615 and vice-provost in 1616.
In 1613, he married Phoebe, daughter of a previous Vice-Provost, Luke Challoner, and published his first work.
In 1634, he imposed on the College an Arminian provost, William Chappell, whose theological views, and peremptory style of government, were antithetical to everything for which Ussher stood.
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. Abbott, Associate Professor of History at Fairfield University, argues that he was an effective and politically important bishop and archbishop.
Ussher went on to become Chancellor of St Patrick's Cathedral, Dublin in 1605 and Prebend of Finglas.
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.
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.