The disappearance of canonical election, the interference of lay patrons, the too frequent use of papal reservations, and the appointment of commendatory abbots and priors, led to a general downfall of discipline in the older religious orders, though there is no evidence to prove that the abuses were as general or as serious as they have been painted. Even at the time when the agents of Henry VIII. were at work preparing the ground for the suppression of the monasteries, and when any individual who would bring forward charges against them could count upon the king's favour, it was only against a few members in less than half a dozen houses that grave accusations were alleged. Even if these accusations were justified, and the circumstances in which they were made are sufficient to arouse suspicions about their historical value, it would not be fair to hold the entire body of religious in Ireland responsible for abuses that are alleged only against the superiors or members of a small number of houses situated in Waterford or Tipperary. Long before the question of separation from his lawful wife had induced Henry VIII. to begin a campaign in Ireland against Rome, the Mendicant Friars had undertaken a definite programme of reform. In 1460 the Bishop of Killala in conjunction with the Franciscan Friar, Nehemias O'Donohoe, determined to introduce the Strict Observance into the Franciscan Houses,[28] and from that time forward in spite of obstacles from many quarters the Observants succeeded in getting possession of many of the old Conventual Houses, and in establishing several new monasteries in all parts of Ireland, but particularly in the purely Irish districts. The Dominicans, too, took steps to see that the original rules and constitutions of the order should be observed. In 1484 Ireland was recognised as a separate province, though the houses within the Pale were allowed to continue under the authority of a vicar of the English provincial, while at the same time a great reform of the order was initiated. Several houses submitted immediately both within and without the Pale, amongst the earliest of them being Coleraine, Drogheda, Cork, and Youghal. The various religious orders of men did excellent work in preaching, instructing the people, in establishing schools both for the education of clerics and laymen, and in tending to the wants of the poor and the infirm. In the report on the state of Ireland presented to Henry VIII. it is admitted that, though the bishops and rectors and vicars neglected their duty, the "poor friars beggers" preached the word of God.[29] That the people and nobles, both Irish and Anglo-Irish, appreciated fully the labours and services of the Friars is evident from the number of new houses which they established for their reception during the fifteenth century. The convents of Longford, Portumna, Tulsk, Burishool, Thomastown, and Gola were established for the Dominicans; Kilconnell, Askeaton, Enniscorthy, Moyne, Adare, Monaghan, Donegal, and Dungannon for the Franciscans; Dunmore, Naas, Murrisk and Callan for the Augustinians, and Rathmullen, Frankfort, Castle-Lyons and Galway for the Carmelites.

The abuses that existed in the Irish Church at this period arose mainly from the enslavement of the Church, and they could have been remedied from within even had there been no unconstitutional revolution. As a matter of fact those who styled themselves Reformers succeeded only in transferring to their own sect the main sources of all previous abuses, namely, royal interference in ecclesiastical affairs and lay patronage, and by doing so they made it possible for the Catholic Church in Ireland to pursue its mission unhampered by outside control. It ought to be borne in mind that the faults of certain individuals or institutions do not prove that the whole organisation was corrupt, and that if there were careless and unworthy bishops, there were also worthy men like the Blessed Thaddeus MacCarthy of Cloyne, who though driven from his diocese by the aggression of the nobles, was venerated as a saint both in Ireland and abroad. The great number of provincial and diocesan synods held in Ireland during the period between 1450 and 1530 makes it clear that the bishops were more attentive to their duties than is generally supposed, while the collections of sermons in manuscript, the use of commentaries on the Sacred Scriptures and of concordances, the attention paid to the Scriptures in the great Irish collections that have come down to us, and the homilies in Irish on the main truths of religion, on the primary duties of Christians, and on the Lives of the Irish Saints, afford some evidence that the clergy were not entirely negligent of the obligations of their office. Had the clergy been so ignorant and immoral, as a few of those foisted into Irish benefices undoubtedly were, the people would have risen up against them. And yet, though here and there some ill-feeling was aroused regarding the temporalities, probates, fees, rents, rights of fishing, wills, etc., there is no evidence of any widespread hostility against the clergy, secular or regular, or against Rome. The generous grants made to religious establishments, the endowment of hospitals for the poor and the infirm, the frequent pilgrimages to celebrated shrines in Ireland and on the Continent, the charitable and religious character of the city guilds, and above all the adherence of the great body of the people to the religion of their fathers in spite of the serious attempts that were made to seduce them, prove conclusively enough that the alleged demoralisation of the Irish Church is devoid of historical foundation.