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 as ‘a learned and grave doctor, able to lay aside his gravity, even in the pulpit; well beloved by scholars for not affecting any sour or austere fashion, either in teaching or governing.’ His mastership, however, was far from being a quiet one. Chadderton's chief opponents among his fellows were W. Middleton, whom he removed from his fellowship in 1575 for sowing discord among the fellows, and Edmund Rockrey, a popular puritan preacher, who refused to attend the holy communion or conform to the ceremonies, for which he was expelled the university, but was afterwards restored to his fellowship by Burghley's interposition (, u.s. pp. 324–45).

In 1579 Chadderton was appointed, through Leicester's influence, to the bishopric of Chester. He was consecrated in the church of St. Gregory by St. Paul's 8 Nov. by Archbishop Sandys. He had already resigned the presidentship of Queens' in the preceding June, and he gave up the regius professorship of divinity the following year, and was appointed to the wardenship of Manchester 5 June 1580, which he held in commendam with the bishopric of Chester. He also held at the same time the rectory of Bangor. He repaid his patron, Leicester, for his elevation by granting him the nomination to the archdeaconry of Chester at the next vacancy. He was at once appointed one of the ecclesiastical commissioners for the discovery and conviction of popish recusants. He took up his residence in Manchester as better suited for the execution of his commission, and remained there until ‘the too frequent jarrings between his servants and the inhabitants of the town’ caused him to remove to Chester (Lansd. MS. 983, f. 129). While resident at Manchester the children of many of the leading families of the diocese were placed under his charge, with the view of guarding them from the seductions of papists. The diocese of Chester included the whole of Lancashire and the north-western portion of Yorkshire, a district still strongly wedded to the old faith, and containing more than a quarter of all the English recusants. We have a very extensive collection of letters written by Lord Burghley, Sir F. Walsingham, Sir Christopher Hatton, and other leading statesmen, during his tenure of the bishopric of Chester, 1581–5, in Peck's ‘Desiderata Curiosa,’ vol. i. bks. iii. iv., chiefly concerning the mode of dealing with the popish recusants, who were to be proceeded roundly with by fine and imprisonment, commending him for the care and pains he had manifested to purge his diocese of the ‘dangerous infection of popery,’ by which it was fondly hoped that taint would ‘in a short time be wholly driven away.’ For his diligent attention to this work he was excused attendance in parliament in 1580. The bishop was not allowed to relax his vigilance for a single moment without a reminder from the privy council or from the primate Sandys (, Annals, iii. bk. i. c. 15, Parker Society;, Sermons, pp. 435–42). ‘Prophesyings or Exercises’ having grown up without any authority, Chadderton issued instructions to regulate them, which are given by Strype (Annals, iii. App. Nos. 38, 39). These exercises were distasteful to the queen, who ordered their suppression. This order was communicated to Chadderton by his metropolitan, Archbishop Sandys, 2 May 1581, with a direct censure for ‘ yielding too much to general fastings, and all-the-day preaching and praying, which the wisest and best could not like, nor could her majesty permit it’ (, bk. iii. No. 29, p. 102). In 1584, when the puritans were once more in favour at court, we find Chadderton censured by the privy council for the scantiness of the religious exercises in his diocese, which he was recommended to use more frequently (ib. bk. iv. No. 41, p. 149). It appears from the registers of the diocese that he was strict in enforcing the use of the cap and the surplice, and suspended some of his clergy for refusing to conform (, Annals, ii. 482). He is described as ‘a learned man and liberal, given to hospitality, and a more frequent preacher and baptiser than other bishops of his time’ (, Mancuniensis, p. 89).

On 5 April 1595 Chadderton was elected bishop of Lincoln, on the translation of Bishop Wickham to Winchester. The election was confirmed on 24 May, and he was enthroned by proxy on 6 June and in person on 23 July. His Lincoln episcopate was uneventful. On Easter day 1603, when James I was making his progress from Scotland to London on his accession, Chadderton preached before the king and court at Burleigh. He continued in his new diocese his endeavours to reduce popish recusants to conformity, and apparently with better success. The registers for 1606–7 contain frequent entries of lay recusants, who had been indicted for not attending their parish church, appearing before him in his episcopal chapel at Buckden and taking the oath of conformity. He complained on his accession that the revenues of the see were in such an impoverished state through the leases granted by his predecessor that he was hard put to it to restore one of his episcopal houses, maintain his household, and keep hospitality. More than 1,000l. was due for dilapidations, of which he could get nothing (Cal. of State Papers, 19 June 1595).