Subsequently, he left Ireland and studied theology at Salzburg and at the Franciscan college at the Catholic University of Louvain.
At the latter place he was, immediately after his ordination, appointed professor of theology, and in that capacity maintained the reputation he had earned as a student.
Opposing both the papal nuncio, Giovanni Battista Rinuccini, and Owen Roe O'Neill, he sought to bring all to the side of the Duke of Ormonde, and imprisoned the members of his own Order at Kilkenny who refused to adopt his views.
This act made him so unpopular that his life was in danger, and he had to be protected by the Earl of Castlehaven at the head of an armed force.
This conduct earned for him the character of a loyalist; but it brought on him the condemnation of John Barnewall, the Minister Provincial of Ireland, together with the guardians of the various communities of friars on the island.