 As procurator to the Archbishop of Salzburg he represented him in 1562 at the Council of Trent and was in line with the thinking of the German bishops in backing a reforming position against the existing church - he supported the foundation of seminaries to train priests, stricter enforcement of clerical celibacy, regular visits by bishops to their dioceses and the unification of liturgy.A series of synods in mid Germany from the 1570s onwards confirmed Ninguarda's reforming ideas, deciding on the foundation of seminaries in Alsace and the County of Tyrol.Even if not all of his ideas were always carried through, Ninguarda remained a fervent supporter of radical change within the Catholic church and was deeply knowledgeable about the reforms of Luther, Zwingli and Calvin, focussing his efforts on the areas they identified as in need of reform.