Religious differences were exacerbated by the fact that the resources of the country were slowly slipping into the hands of the English-Protestant community. They held all administrative and judicial offices in Ireland, and a number of clergy had been recruited in England and Scotland to take up positions in the established Protestant church. The result of this was the development in Ireland of two distinct communities, one Protestant and primarily of British origin and the other Catholic and principally Irish-born (Canny, Nature). The continued rise of Protestant dominated English portended the onset of religious persecution in Ireland. Thus, 1641 can be regarded as a strike by "Catholic" Ireland in an endeavour to overthrow the Protestant regime in Ireland. The political debate of pre-1641 Ireland about the extent to which legal toleration should be provided to Catholicism added to growing separation and angst between the two religious communities.
The anti-Catholic legislation passed by the parliament of 1613-1615 is in direct relation to the emergence of a distinct national identity in early modern Ireland. By securing the rigorous enforcement of the Oath of Supremacy, the implementation of recusancy fines, the expulsion of all Catholic priests from Ireland, and the confiscation of Catholic lands, the New English government systematically excluded Catholics from political and social influence on the grounds of religion (Aidan, Colonial Identity). Unlike the Irish, the Protestants followed the beliefs of uncompromising Calvinism with an emphasis on Puritan values that reinforced the growing anti-Roman Catholic movement in England under Charles I. However, in 1632 Charles appointed Thomas Viscount Wentworth as deputy of Ireland, who was not as zealous in his prosecution of the Catholic Church (Perceval-Maxwell, Outbreak). The .
infrastructure of the Catholic Church was in fact strengthened in the 1630s through tolerated private practice of Catholic services and the strengthening of a Catholic "Old English," or established English settlers, position in Parliament.