Mary died in 1558 and was succeeded by her half sister Elizabeth, Henry's child by Anne Boleyn. Elizabeth was a politique, that is, she was someone who placed royal prerogatives in the political order above religious or traditional considerations. While she was not moved by Protestant principles and could tolerate accommodation with Catholics, the maintenance of her ascendancy in all her realm was her first concern and that required her maintenance of supremacy in the church. Accordingly, in Ireland she had the lord lieutenant, the earl of Sussex, summon a parliament, which in less than a month imposed the complete reformation on the church in Ireland. Significantly, unlike the Irish parliaments in Henry's time, there were almost no Gaelic peers in attendance and a substantial number of the bishops were absent. Even the territorial representatives who made up the House of Commons came largely from only 10 counties, primarily in Leinster, and 28 towns. Ulster and Connacht were all but unrepresented. The parliament passed an Act of Supremacy, which stated that the queen was the head on earth of the Church of Ireland. All officeholders in church and state, all mayors of towns, all those taking university degrees, and all tenants in chief of the queen (that is, all lords including those who had gained their land and title as a consequence of "Surrender and Regrant") were required to take an oath acknowledging her status. Also passed was an Act of Uniformity, which imposed the new Book of Common Prayer on all the clergy, made English the language of the prayer book, and made attendance at the state church compulsory on pain of a fine.
These developments worked to change the landscape of loyalties in Ireland and would ultimately draw together, in their allegiance to Catholicism, the Irish and the Old English who had been contesting against each other for centuries. The Old English were especially incensed, as they had been loyal to the Crown, basing their own position on their adherence to English law. The Gaelic chieftains had given periodically their allegiance to the king as "lord" of Ireland, and had gone through the motions of "Surrender and Regrant," but they remained temperamentally committed to the Brehon tradition, with the implications that their holdings belonged to the sept or family and that election rather than primogeniture was the basis of succession. They were warrior chieftains who drew on the feudal contributions and military services of both their subordinates and the common folk, who possessed varying degrees of freedom. In many ways their system was an anachronism, a throwback from the modern world of commerce and settled agriculture that the "New Monarchy" had brought to England and was attempting to bring to Ireland. The Anglo-Irish were better adapted to implement the new system, except for the religious question. Accordingly, their place in public life would increasingly be taken by the "New English," settlers who arrived as civil servants sent over from England and who in course of time became officials, churchmen, and landlords.
This was the period in which the energies of the Counter-Reformation, the Catholic attempt to reform the church and undo the spread of Protestantism, was well underway in Europe. The instrument that was especially employed to that end was education, as it was primarily Catholics who began the schools in Ireland that had been called by an act of 1538 to be set up to promote the English language. In addition, attendance at Catholic colleges on the Continent began, which became a regular pattern for Irish Catholics seeking higher education, especially in preparation for the priesthood. A persistent number of missionaries, especially Jesuits, began to make their way to Ireland to defend the "True Faith," although an earlier Jesuit mission to Ireland in the 1540s had met little response and had to be diverted to Scotland. The work of the other friars, the Franciscans, Dominicans, and Augustinians, also persisted and did much to make Ireland the intensely faithful Catholic nation it would become. The general effect was to make the Act of Uniformity unenforceable in most cases.