1576 he vacated his fellowship at Christ's by marriage with Cecilia, daughter of Nicholas Culverwell, Queen Elizabeth's merchant for wines. The Culverwell family were strong puritans; two of Mrs. Chaderton's sisters were married to well-known members of the same party, Dr. Whitaker and Thomas Gouge, and her brothers Samuel and Ezekiel Culverwell were famous puritan preachers. Chaderton continued to reside and preach at Cambridge, and to take part in university matters. He took the degree of B.D. in 1578, and in 1581 was engaged in a controversy with Peter Baro [q. v.], who had published some theses concerning ‘justifying faith,’ which Chaderton denounced in a sermon. Baro cited Chaderton before the vice-chancellor, who heard the controversy, which was conducted with less than the usual acrimony. In 1584 Sir Walter Mildmay, who had, like Chaderton, been at Christ's, and had since acquired great wealth in a long course of public employments, determined to devote a portion of his riches to the foundation of a college at Cambridge especially designed to train up ‘godly ministers.’ Sir Walter, who was chancellor of the exchequer and a privy councillor, was well known to have sympathies on the side of the puritan party. For the mastership he selected Chaderton, whose character he respected, and with whom he was personally acquainted. When Chaderton hesitated (having been offered better preferment), he said, ‘If you won't be master, I won't be founder.’ Chaderton accepted the office, and fully justified Sir Walter's choice. Though a noted puritan, he was also a churchman, and never joined in the cry against ‘prelacy,’ though he refused to accept a bishopric himself. He was prebendary of Lincoln from 1598 till death. He ruled the new college with great credit and success for thirty-eight years, speedily attracting to it fresh benefactions, and many students, especially from families in sympathy with the Calvinistic puritans. During his mastership he was employed on the Cambridge committee for drawing up the authorised version of the Bible of 1607–11; and, earlier, was with three others chosen to represent the ‘Millenary Plaintiffs’ at the Hampton Court conference, where he was somewhat rudely assailed by his old fellow-collegian and friend, Richard Bancroft [q. v.], then bishop of London, who denounced him and his fellow-commissioners to the king as ‘Cartwright's schollers, schismatics, breakers of your laws; you may know them by their Turkie grogram.’ Chaderton was moderate, and pleaded rather for concessions to weak consciences than for radical changes. This moderation characterised him throughout, although his chosen friends were the leaders of the extreme party, such as Cartwright, Perkins, and Whitaker. In October 1622 he resigned his mastership, apparently under some pressure from the fellows, who wished to have Dr. Preston, a fellow of Queens', as his successor. Preston was chaplain to Prince Charles, and intimate with Buckingham; and the fellows thought that his influence at court might secure to them the abolition of one of their statutes, which they especially disliked, and which Chaderton supported, compelling them to reside and to vacate their fellowships at the standing of D.D. The old man was persuaded that by his resignation Preston's election could be secured, and the danger of an Arminian being put in his place by royal mandate be avoided. He accordingly resigned on 26 Oct. 1622, and Preston was elected. He survived his resignation eighteen years, living in the town near the college, and in spite of his great age continuing his devotion to his old studies, and especially to botany. His wife died in 1631, but his only daughter, who married the son of Archdeacon Johnson, founder of Oakham and Uppingham schools, remained with him until his death. He preserved in a remarkable degree his bodily and mental faculties to the last. His biographer, Dillingham, says that near the end of his life he saw him reading a Greek Testament of very small type without glasses; and that, though he watched for it, he never detected him repeating himself in his conversation. Prince Charles and Frederic the Elector Palatine visited him in 1613, and insisted on his taking his doctor's degree, from which he had always shrunk. In 1615 James I visited and conversed with him, and two of his old pupils who had risen high in political life took especial pains to show him honour—Finch, the lord-keeper, and Rich, the ill-fated Earl of Holland. He died on 13 Nov. 1640, aged 102 or 103 years, and was buried in the Emmanuel College chapel; his body was removed to the new chapel built after the Restoration by Sir Christopher Wren.
He does not appear to have published any work except one small tract printed anonymously, and reprinted with others by Ant. Thys of Leyden, ‘de justificatione coram Deo et fidei perseverantia, non intercisa.’ Baines, in his ‘History of Lancashire,’ mentions a sermon and other works, which appear however to have been in manuscript, as also some mentioned by Dillingham, viz. the theses against Baro; two treatises, ‘De Cœna Domini,’ and ‘De Oratione Dominica;’ and some lectures on logic and on Cicero.