Lyon, William (d. 1617), was the first protestant bishop of Cork, Cloyne, and Ross. Little is known of his background or early life, apart from the fact that he was born in Chester. He may have gone to Oxford, though some sources claim he began his career as an innkeeper or a seaman. He arrived in Ireland c.1570 and was presented to the vicarages of Naas (6 November 1573) and Bodenstown (23 July 1580), though he was granted permission (24 November 1577) to hold these while living in England. He served (1580–82) as chaplain to the lord deputy, Arthur Grey (qv), and was appointed to the see of Ross (nominated 30 March, letters patent 12 May 1582). To this he added Cork (in commendam, November 1583), and then on 24 March 1586 Cork, Ross, and Cloyne were all annexed and granted to him.
Lyon regularly reported on conditions in Munster to the government, and served on the commissions for ecclesiastical causes throughout the 1580s and 1590s. He struggled manfully against the background of the Desmond rising, the Nine Years War, and the growing strength of the counter-reformation, to build up the established church, especially around his seat at Ross, where he erected a house, church, and school, and distributed copies of the New Testament and prayer book. But success was limited. School books were vandalised; his church was destroyed in a rising; and – once official sanctions against recusancy were lifted in the mid 1590s, and pressure from the local catholic population and seminary priests grew – the native ministers and their parishioners fled the Church of Ireland. Lyon reported how ‘within these two years ... where I have had a thousand or more in a church at sermon, I now have not five’ (PRO, State Papers, 63/183/47). He attributed the decline to the government's failure of nerve in relaxing the laws against recusancy in order to preserve the loyalty of catholics during the Nine Years War; and he wrote in 1595 to both Burghley and the lord deputy to complain of their failure to fight the catholic Antichrist.
By 1604 the situation was even worse: his dioceses were ‘overwhelmed with the palpable darkness of idolatry’ (PRO, State Papers, 63/221/35A); the sacraments were administered entirely by catholic clergy; there was, he felt, hardly the face of an established church left. After an abortive attempt by Henry Brouncker (qv), lord president of Munster 1604–7, to restore conformity by the imposition of harsh penalties, and sporadic subsequent attempts to fine recusants, the Church of Ireland in Munster switched its attention to the settler community. The restoration of the plantation, after the disasters of the Nine Years War, enabled Lyon to attract a considerable number of English (often graduate) clergy, and by 1615 his three dioceses had seventy-three resident clergy, of whom thirty-eight were preachers. Throughout his episcopate he sought to restore the parlous finances of his sees. Cloyne was in a particularly impoverished state, its estates having been granted away by Lyon's predecessor for a minuscule annual rent of £3 6s. 8d. Lyon used the law courts and tried to secure acts of parliament in order to regain these and other alienated lands. He had some success, but Cloyne eluded him. Nevertheless he did succeed in increasing the revenues of his sees from £70 (when he first became bishop) to £200 by 1615, and restored the bishop's house in Cork at a cost of over £1,000. He died 4 October 1617 and was buried in Cork cathedral. All we know of his family is that he had a wife, Elizabeth; a son, William; and two daughters, Mary and Elizabeth.