He was a noted controversialist who doggedly defended the English Church from both Puritan and Roman Catholic accusations, as well as the materialism of Thomas Hobbes.

As a royal commissioner, he worked to obtain the surrender of fee farms on episcopal and clerical revenues, recovering church income.

The ninety-fourth canon, endorsing a policy of William Bedell, bishop of Kilmore, provided for the use of the bible and prayer book in the vernacular in an Irish-speaking district; this was opposed by Bramhall.

In August 1636 Bramhall at Belfast assisted Bishop Henry Leslie against the five ministers who would not subscribe to the new canons (see Edward Brice).

[2] He employed the proceeds of his English property in purchasing and improving an estate at Omagh, County Tyrone, in a Catholic area.

In the same year, he was made receiver-general for the crown of all revenues from the estates of the city of London in his diocese, forfeited through non-fulfilment of conditions of the holding.

In 1639 he protected and recommended to Wentworth John Corbet, minister at Bonhill, who had been deposed by the Dumbarton presbytery for refusing to subscribe to the assembly's declaration against prelacy.

The Irish commons in October 1640 drew up a remonstrance, in the course of which they speak of the Derry plantation as 'almost destroyed' through the policy of which Bramhall was the administrator.

[2] After the English House of Commons had impeached Wentworth (now earl of Strafford) of high treason on 11 November 1640, the Ulster presbyterians drew up a petition to the English parliament (presented by Sir John Clotworthy about the end of April 1641), containing thirty-one charges against the Irish Anglican prelates, and asking that their exiled pastors might be reinstated.

[2] In 1642, he returned to England, and was in Yorkshire until the battle of Marston Moor (2 July 1644); he supported the royalist cause by preaching and writing, and sent his plate to the king.

He then went back to Ireland, but not to Ulster, in 1648; at Limerick he received in 1649 the profession of the dying James Dillon, 3rd Earl of Roscommon.

[2] Although Parliament passed declarations requiring conformity to the episcopacy and the liturgy, and ordering the burning of the Covenant, Bramhall could not carry his bills for a uniform tithe system, and for extending episcopal leases.

[2] Bramhall was defending his rights in a court of law at Omagh against Sir Audley Mervyn when a third paralytic stroke deprived him of consciousness.

He followed this with his 1649 Fair Warning against the Scottish Discipline, which was an attack on the weaknesses of the presbyterian model and an excoriation of the Puritan religious claims.

The posthumous publication of Bramhall's Vindication of himself and the Episcopal Clergy from the Presbyterian Charge of Popery, as it is managed by Mr. Baxter, &c., 1672, with a preface by Samuel Parker, produced Andrew Marvell's 'The Rehearsal Transpros'd,' 1672.