Within the walled city of Cork there were two churches. The principal church of the city was Christ Church, also called Holy Trinity, on the South Main Street. The church was on the site of today's deconsecrated church that now houses the Triskel Arts Centre. The English crown had the patronage of the church.The other church was Saint Peter's, which was roughly on the site of another deconsecrated church on the North Main Street that is now home to the Cork Vision Centre. Saint Peter's was a prebend of the archdeacon of Cork. There were chapels attached to both churches, where chantry priests said masses for the repose of the souls of the dead. Civic functions were held in Christ Church. While the patronage of Christ Church was nominally in the hands of the English crown, in practice, members of the merchant patriciate dominated both churches and frequently buried their dead in the grounds of the churches.
Outside the walls of the city were the religious houses of the Dominicans, Franciscans and Augustinians. The ancient monastery of Gill Abbey was also still in existence, although an inquisition in the 1530s found that there was only one monk in occupancy.
The unity of European Christendom was fractured by the Reformation of the sixteenth century, one of the most momentous events in the history of Europe, which was sparked by 95 theses presented by Martin Luther at Wittenberg in 1517 condemning corruption and practices that did not seem to him to have a biblical foundation. The history of the Reformation in Cork is as complicated and as tortuous as the history of the same event in any other part of Europe.
In 1536, the Irish Parliament declared Henry VIII of England the supreme head of the church in Ireland. In that same year, Henry made Dominick Tirry, rector of Shandon, the bishop of Cork. Tirry repudiated papal supremacy and acknowledged the authority of Henry. In 1541, two officials from England arrived in Cork to administer the dissolution of the houses of the religious orders in Cork. A local jury, composed mainly of members of the local merchant oligarchy, decreed the demolition of the religious buildings associated with the orders and the secularisation of their properties.
The papacy appointed rival bishops to those loyal to the Henrician reforms, but none of them could re-establish their authority over the city. In 1557, the Irish Parliament re-established Roman Catholicism as the religion of the country, after the accession of Queen Mary in 1553 in England. However, after the accession of Elizabeth I to the throne in 1558, the Irish Parliament once again acknowledged the temporal and spiritual supremacy of the English monarch. Elizabeth I confirmed Roger Skiddy as Bishop of Cork. Skiddy subsequently resigned as bishop and was awarded the Wardenship of Youghal. It should be understood that many of the first Church of Ireland bishops of Cork were still deeply attached to the rites and liturgy of the Roman Catholic Church and the situation for both clergy and laity was very confusing.
The first truly zealous Protestant Bishop of Cork appears to have been Matthew Sheyne, who was appointed bishop in 1572. Sheyne caused great consternation among the population of the city by publicly burning a much-venerated statue of Saint Dominic at the market cross in Cork in 1578. On Sheyne's death in 1582, the equally zealous William Lyon, who was already Bishop of Cloyne and Ross, succeeded him.
The Papacy made a shrewd appointment in 1580 by appointing Dermot Creagh as Roman Catholic Bishop of Cork. Creagh, fired by zeal for the Counter-Reformation, used the disaffection caused by the Munster plantation to woo back the population to the old faith. He succeeded to such an extent that in 1603 some of the leading citizens of Cork burned Church of Ireland bibles and service books and attempted to restore the mass in the city's churches.
By the end of the sixteenth century, the old merchant patriciate was once again predominantly Roman Catholic. This was in marked contrast to the settlers who had come to Cork during the Munster plantation and who were loyal to the Anglican tradition. A poisonous religious divisiveness has been added to a society already fissured along the lines of ethnicity and class.