Subsequently Pearson joined the last remnant of Charles I's party in the west, acting as chaplain in 1645 to Goring's forces at Exeter (Sherman, Hist. MS. Coll. Jesu, Cantabr. p. 407). On the collapse of the royal cause he withdrew to London, where he seems to have remained till the Restoration, devoting the greater part of his time to his studies. He had lost the revenue of his prebend as early as 1642, and had resigned or been deprived of his rectory four years later; but the possession of a small patrimony in Norfolk freed him from extreme privations, and enabled him to maintain two younger brothers at Eton. Moreover, patrons gave him pecuniary assistance. He is said to have been for a time chaplain to Sir Robert, the eldest son of Sir Edward Coke, and subsequently to George, lord Berkeley, and his son of the same name and title, afterwards first Earl of Berkeley. In 1654 he accepted an invitation from the inhabitants of St. Clement's, Eastcheap, to deliver a weekly sermon in their parish church. This he appears to have regularly continued up to the Restoration, without receiving any pecuniary recompense. It was at St. Clement's that he preached in substance the series of discourses which he published in 1659 under the title of ‘An Exposition of the Creed,’ a work which is, within its limits, the most perfect and complete production of English dogmatic theology. Evelyn writes in his ‘Diary,’ 15 April 1655: ‘In the afternoon Mr. Pierson (since bishop of Chester) preached at East Cheap, but was disturbed by an alarm of fire, which about this time was very frequent in the city.’
While debarred from the full exercise of his ministry, Pearson defended the church with his pen against both Romanist and puritan assailants. In a preface to Lord Falkland's ‘Infallibility of the Church of Rome,’ he pointed out some singular admissions made by Hugh Paulinus Cressy [q. v.], a recent convert to the Roman catholic communion; and in 1649 he published a short tract, entitled ‘Christ's Birth not mistimed,’ in refutation of an attempt made by some of the church's opponents to throw discredit on the calculation by which Christ's nativity is observed on 25 Dec. He also interested himself in promoting the polyglot Bible, which appeared in 1654–7, under the editorship of Brian Walton [q. v.] (see Evelyn, Diary, 22 Nov. 1652). It does not, however, appear that Pearson had any literary share in this undertaking. He only gave or obtained for it pecuniary aid.
Pearson's reputation as a scholar was soon established, and his commendation was considered sufficient evidence of the value of a work. Prefaces by him were published with Meric Casaubon's edition of Hierocles, Stokes's ‘Explication of the Minor Prophets,’ and John Hales's ‘Remains.’ In 1657 Pearson, with his friend Peter Gunning [q. v.], engaged in a conference with two Roman catholics on the question whether England or Rome was guilty of schism at the Reformation. A garbled account of this controversy, under the title of ‘Schism Unmaskt,’ appeared in the following year.
After the Restoration, Pearson was collated by Juxon to the rectory of St. Christopher-le-Stocks in the city of London on 17 Aug. 1660, and in the same month Bishop Wren made him a prebendary of Ely. On 26 Sept. Brian Duppa, bishop of Winchester, conferred upon him the archdeaconry of Surrey, which he retained till his death. About this time he proceeded to the degree of D.D., and was appointed a royal chaplain, and on 30 Nov. he received from the patron, Bishop Wren, the mastership of Jesus College, Cambridge.
In February 1661 Pearson was one of the Lent preachers at court, and three months later one of the posers at the annual examination of the Westminster scholars (Evelyn, Diary, 13 May). In the spring and summer of this year he took an active part in the Savoy conference, where his courtesy and forbearance won the respect of his opponents. He was the only champion of episcopacy whom Baxter notices favourably. ‘Dr. Pierson,’ he says, ‘was their true logician and disputant. … He disputed accurately, soberly, and calmly, being but once in any passion, breeding in us a great respect for him, and a persuasion that if he had been independent he would have been for peace, and that if all were in his power it would have gone well.’
Pearson sat in the convocation which met in May 1661, when he was chosen, with John Earle, to superintend a version into Latin of the amended Book of Common Prayer; he also took part in drawing up the service for 29 May, and the prayer for parliament, and was one of three to whom the revision of all the additions and amendments of the prayer-book was committed prior to its acceptation by both houses. By order of the upper house he prepared in 1664 a Latin and Greek grammar to be used in all the schools of England.
Meanwhile, in June 1661, he succeeded Gunning as Margaret professor of theology at Cambridge, and hereupon he resigned his stall at Salisbury and his London living.
