as chaplain to Ireland in 1633. He was made dean of Waterford by patent, 25 May 1635, and in October was presented by the crown to the rectory of Armagh in Cavan, as 'one of the chancellor's chaplains' (Lib. Munerum, pt. v.) He resigned Armagh in 1637, and in that year became rector of Galloon or Dartry in Monaghan (Shirley, p. 328), prebendary of the Holy Trinity in St. Finbar's, Cork, and dean of Derry. While Margetson held this deanery, 500l. was granted by the crown to provide bells for his cathedral; and Laud wrote to Strafford on 10 Sept. 1638, 'Out I am of the hearing of Londonderry bells, but I am glad they are there.' In December 1639 Margetson was made dean of Christ Church, Dublin. No new dean of Derry was appointed until after the Restoration. It appears from the correspondence between Laud and Strafford that the latter intended to restore the almost ruinous cathedral of Christ Church, but that he found neither time nor money. Margetson was prolocutor of the lower house of convocation in 1639.
When the rebellion of 1641 broke out, Margetson, himself distressed from the failure of income, was yet busy in helping those whose need was still greater. In August 1646 he signed the document in which eleven bishops and seventy-seven other clergymen congratulated Ormonde upon the conclusion of peace, and thanked him for his efforts in their behalf, 'without which many of us had undoubtedly starved' (Carte, Letter 471). A year later Dublin was in the hands of the parliament, and the Anglican clergy were invited to use the directory instead of the Book of Common Prayer. One bishop and seventeen clergymen, of whom Margetson was one, signed the dignified and spirited answer in which they refused to hold their churches on these terms (Mason, bk. ii. chap, iii.)
Ormonde left Ireland 28 Aug. 1647, and Margetson fled to England about the same time. He suffered imprisonment at Manchester and elsewhere, but was afterwards allowed to live in London unmolested, but very poor. He was employed by the wealthier cavaliers to dispense their alms among distressed loyalists in England and Wales, and William Chappell [q.v.], bishop of Cork, Milton's old tutor, is said to have been relieved by him.
With the Restoration Margetson's fortunes revived. On 25 Jan. 1660-1 he was made archbishop of Dublin by patent, and was allowed to hold his old living of Galloon, his Cork prebend, and the treasurership of St. Patrick's, Dublin, along with the archbishopric. He was consecrated in St. Patrick's two days later, along with eleven other bishops-elect, certainly one of the most imposing ceremonies of this kind on record (ib. bk. ii. chap, iv.) He was also made a privy councillor. In 1662 and 1663 he let on lease for twenty-one years his Cork property (Caulfield).
Margetson was translated to Armagh in 1663, where he succeeded Bramhall, who is said to have recommended him on his deathbed to Ormonde as the fittest man for the primacy. Harris throws doubts on this story, but perhaps groundlessly (Mant, chap. ix. sec. ii.) In 1667 he succeeded Jeremy Taylor as vice-chancellor of Dublin University, and remained in office till his death; but academical duties, though performed with care and success, did not prevent him from attending to his own diocese. Armagh Cathedral had been burned by Sir Phelim O'Neill in 1642, and Margetson lived to see it rebuilt. The subscriptions falling far short of what was wanted, he made up the deficit himself. He also founded a free school at Drighlington, his native place. Margetson always refused to invest, even on the most tempting terms, in any land which had ever belonged to the church. His generosity was at all times remarkable, and he sought no credit for it. In the same modest spirit he kept his great learning in the background. In the winter of 1677 he became disabled by obstinate jaundice, but nevertheless insisted on communicating publicly in the following May. He died in Dublin, 28 Aug. 1678, after enduring great pain with remarkable patience, and was buried within the altar-rails of Christ Church. His charity and exemplary life had won him such reputation that all sorts and conditions of men resorted to his deathbed to receive his last blessing. At his funeral Dr. Palliser spoke of his conciliatory attitude towards theological opponents. He was reverenced and beloved by his clergy, to whom he was both kind and strict, and he could scarcely blame one of them without weeping, 'for the vices of the clergy touched his very heart-strings.'
Margetson's eldest son, John, was killed at the siege of Limerick, being then a major in William's army, leaving a daughter, Sarah, from whom the earls of Bessborough and Mountcashel are descended. The Earl of Charlemont is descended from Anne Margetson, the primate's only daughter.