 In 1577 Ninguarda was made bishop of Scala and in 1583 was transferred to be bishop of Sant'Agata de' Goti.His fellow-Dominican pope Pius V (who had visited the convent of Sant'Antonio at Morbegno and had a profound knowledge of the Valtellina and its frictions between Protestant and Catholic) and then pope Gregory XIII (of whom Ninguarda was a confidant) then utilised him for the difficult beginnings of the Counter Reformation in Germany, Austria and Bohemia, at first as visitor to the convents of all orders, then as papal nuncio to mid Germany (1578–82) and Switzerland (1586–88).As nuncio he travelled through Bavaria, Austria and Switzerland.