The Protestant Reformation was introduced into Ireland in the 1530s but made little progress in winning converts among the indigenous Irish population. King James I was, however, a committed member of the Church of England and was concerned to promote the established church in Ireland. Consequently, religious reformation was central to the ideological framework of the Plantation scheme. One of the criteria for the selection of undertakers and tenants was that they be conformable in religion. Each portion in the Plantation was designated a parish in the established church and provision for parochial land was incorporated into the scheme. In addition, each county was to have a royal school for the education of young men, some of whom it was hoped, would later attend Trinity College Dublin to train as Protestant ministers. The university was also given a generous grant of land on the escheated lands in order to ensure its long-term economic viability.
The new settlers enthusiastically supported the religious programme incorporated into the Plantation scheme. Individual landlords built or restored churches at their own expense and provided for ministers to service them. The number of resident Protestant clergy in Ulster increased significantly in the early 17th century. Many came from Scotland where they had been ordained as Presbyterian ministers in the Scottish church. In Ireland, despite their Presbyterian background, they became ministers in the Church of Ireland. It was not until 1642 that a separate Presbyterian Church was formed in Ireland.
Presbyterianism fostered an active lay involvement in church affairs. Weekly prayer meetings and small group discussions on the Scriptures were encouraged, as was regular attendance at Sunday sermons. In the absence of a church, meetings were held in the home or in an outbuilding on a farm. The strength of the religious commitment of the Ulster Presbyterian community was demonstrated in the 1620s when a religious revival took place in the Six-Mile-Water area in County Antrim. Initiated by a popular preacher, James Glendinning, the movement expanded as more ministers joined and hundreds of people walked upwards of 20 miles to listen to preachers and pray together for several days at a time. Even critics of Presbyterianism in Ulster were impressed by the religious fervour of the ministers and the laity.
Sir Thomas Wentworth (later the Earl of Strafford), Lord Deputy in Ireland, 1633-1641 disliked the Presbyterian orientation of the church in Ulster and he dismissed many of the Scottish clergy in the 1630s, an action which only served to strengthen the Presbyterian ethos of the settler community as it perceived itself to be under siege from members of the Roman Catholic as well as of the established church.
Wentworth was not as zealous in his prosecution of the Catholic Church as he was of dissident ministers within the established church. The infrastructure of the Catholic Church was in fact strengthened in the 1630s and, although Catholic laymen were banned from holding public office, the Dublin government tolerated private practice of Catholic services. The number of resident clergy increased during this time and played an important role in encouraging popular support for the rebellion in 1641.