While St. Leger was not slow in taking measures to resist a foreign invasion, he did not neglect the instructions he had received about introducing the Book of Common Prayer in place of the Mass. He procured several copies of the English service and sent them to different parts of the country, but instead of having it translated into Irish he had it rendered into Latin for the use of those districts which did not understand English, in the hope possibly that he might thereby deceive the people by making them believe that it was still the Mass to which they had been accustomed. Apparently, however, the new liturgy met with a stubborn resistance. In Limerick, although the city authorities were reported to be favourable, the Bishop, John Quinn, refused to give his consent to the proposed change, and throughout the country generally the Deputy was forced to confess that it was hard to plant the new religion in men's minds. He requested that an express royal command should be addressed to the people generally to accept the change, and that a special commission should be given to himself to enforce the liturgy.[82]

The formal order for the introduction of the English service was forwarded to St. Leger in February 1551, and was promulgated in the beginning of March. Bishop Quinn of Limerick was forced to resign the temporalities of his See to make way for William Casey, who was expected to be more compliant. A number of bishops and clergy were summoned to meet in conference in Dublin to consider the change. At this conference the reforming party met with the strongest opposition from the Primate of Armagh. Although George Dowdall had accepted the primatial See from the hands of the king and had tried to unite loyalty to Rome and to Henry VIII., he had no intention of supporting an heretical movement having for its object the abolition of the Mass. From the very beginning of the Protector's rule he had adopted an attitude of hostility to the proposed changes, as is evident from the friendly letter of warning addressed to him by the Lord Deputy Bellingham.[83] The Primate defended steadfastly the jurisdiction of the Bishop of Rome, and refused to admit that the king had any authority to introduce such sweeping reforms by virtue of his office. Finding that his words failed to produce any effect on the Deputy he left the conference, together with his suffragans, except Staples of Meath, and repaired to his own diocese to encourage the people and clergy to stand firm. St. Leger then handed the royal commission to Browne, who declared that he submitted to the king "as Jesus Christ did to Caesar, in all things just and lawful, making no question why or wherefore, as we own him our true and lawful king."[84]

Though St. Leger pretended to be a strong supporter of the new religion, yet, according to Archbishop Browne, he contented himself with the formal promulgation of the royal orders. He himself on his arrival in Ireland assisted publicly at Mass in Christ's Church, "to the comfort of his too many like Papists, and to the discouragement of the professors of God's word." He allowed the celebration of Mass, holy water, Candlemas candles, and such like to continue in the diocese of the Primate and elsewhere without protest or punishment. He seemed, even, to take the side of the Primate at the council board, and sent a message to the Earl of Tyrone "to follow the counsell and advice of that good father, sage senator and godly bishop, my lord Primate in everything." He went so far as to present the Archbishop of Dublin with a number of books written in defence of the Mass and Transubstantiation, and when the archbishop ventured to remonstrate with him on his want of zeal for God's word the only reply he received was, "Go to, go to, your matters of religion will mar all."[85] St. Leger's main object was the pacification of the country and the extension of English power, both of which, he well knew, would be endangered by any active campaign against the Mass.

St. Leger was recalled, and Sir James Crofts, who had been sent on a special commission to Ireland a few months earlier, was appointed Deputy in his place (April 1551). His instructions in regard to the Book of Common Prayer and the inventory of the confiscated church plate were couched in terms similar to those given to his predecessor.[86] Anxious from the beginning to conciliate Primate Dowdall, he forwarded to him a respectful letter (June 1551) calling his attention to the respect paid by Christ Himself and St. Peter to the imperial authority, offering his services as mediator between the Primate and his opponents, Browne and Staples, and warning him of the likelihood of much more serious changes, which he (the Deputy) pledged himself if possible to resist.[87] To this communication the Primate sent an immediate reply, in which he offered to meet his opponents in conference, though he could hold out no hope of agreement, as their "judgments, opinions, and consciences were different."[88]