In July 1556 Lord Fitzwalter was sent to Ireland as Deputy. "Our said Deputy and Council," according to the royal instructions, "shall by their own good example and all other good means to them possible, advance the honour of Almighty God, the true Catholic faith and religion, now by God's great goodness and special grace recovered in our realms of England and Ireland, and namely they shall set forth the honour and dignity of the Pope's Holiness and Apostolic See of Rome, and from time to time be ready with our aid and secular force, at the request of all spiritual ministers and ordinaries there, to punish and repress all heretics and Lollards, and their damnable sects, opinions, and errors." They were commanded, too, to assist the commissioners and officials whom Cardinal Pole as papal legate intended to send shortly to make a visitation of the clergy and people of Ireland.[6] On the arrival of the new Deputy in Dublin he went in state to Christ's Church to assist at Mass, after the celebration of which he received the sword of state from his predecessor before the altar, and took the oath in presence of the archbishop. "That done, the trumpets sounded and drums beat, and then the Lord Deputy kneeled down before the altar until the Te Deum was ended."[7]

The new Deputy was instructed to take measures for summoning a meeting of Parliament in the following year to give legal sanction to the restoration of the Catholic religion, and to deal with the ecclesiastical property that had been seized. Possibly in the hope of securing some of these again for the Church a commission was issued to the Archbishop of Dublin, the Bishop of Kildare, and a number of clerics and laymen "to inquire concerning the chalices, crosses, ornaments, bells, and other property belonging to the parish churches or chapels in the county of the city and county of Dublin and of sales made thereof to any person or persons, the price, in whose hands they then remained, and also in whose possession were the houses, lands, and tenements, belonging to those churches." Similar commissions were issued to others for the counties of Drogheda and Louth, Kildare, Carlow, Wexford, Kilkenny, Meath, Westmeath, Waterford, Tipperary, Limerick, Cork, and "for the county of Connaught."[8]

In June 1557 the Irish Parliament met. A Bull of absolution from the penalties of heresy and schism was read by the Archbishop of Dublin on bended knees, while the Lord Deputy, officials, and members, both Peers and Commoners, knelt around him. When this ceremony was finished all retired to the cathedral, where the Te Deum was sung in thanksgiving, and all pledged themselves as a sign of their sincere repentance to abolish all the laws that had been passed against the Holy See. The acts prejudicial to the rights of the Pope enacted since the year 1529 were abolished. The title of supreme head of the church, it was declared, "never was or could be justly or lawfully attributed or acknowledged to any king or sovereign governor, nor in any wise could or might rightfully, justly, or lawfully, by the king or sovereign governor of the same realms, be claimed, challenged, or used." "All Bulls, dispensations, and privileges obtained before the year 1529 or at any time since, or which shall hereafter be obtained from the See of Rome, not containing matter contrary or prejudicial to the authority, dignity, or pre-eminence royal or imperial of these said realms or to the laws of this realm" were allowed to be "put in execution, used, and alleged in any civil court in Ireland and elsewhere." The jurisdiction of the bishops was restored, the laws against heresy passed in the reign of Richard II. and Henry IV. were renewed, and the payment of First Fruits was suppressed. Care was taken, however, to avail of the dispensation granted by the Holy See, whereby those who had obtained possession of the property of churches and monasteries should not be disturbed, although it was enacted that none of the laymen who had obtained such grants could plead the rights of exemption enjoyed by some of their former owners against the jurisdiction of the bishops, and that notwithstanding the Statutes of Mortmain those who then held "manors, tenements, parsonages, tithes, pensions or other hereditaments" might bequeath or devise them to any spiritual body corporate in the kingdom, such clause to have the force of law for twenty years.[9]