When the Protestant Reformation began to gather steam, the Catholic Church set about creating its own institutional reforms, in an effort to revitalize itself and keep its members. The Council of Trent (1545–63) modernized the Church in Europe, but Ireland was slow to implement these modernizations.

The pope watched the Reformation in England with great interest. He didn't want to lose Ireland, too. In 1606, the pope congratulated the Irish for sticking to their religion, and the Church leaders in Ireland decided it was time to modernize their parishioners.

The pope sent the Jesuits, a new group of Catholic missionary priests, to take on this project; the Jesuits found Irish Catholicism very strange. Not only was it full of odd Celtic rituals, the Irish Church itself was divided into an old Gaelic form, which rejected interference from Rome, and the (newer) Old English form, which embraced Roman doctrine.

The Jesuits worked on getting Irish priests to stop drinking and marrying, and encouraged the Catholic people to avoid Protestants. Although the Irish resisted change and persisted in holding their traditional wakes and casual marriages, the Catholic Church in Ireland did increase its presence and modernize some practices. The traditional Irish flexibility and adaptability proved useful in the survival of the institution.