 Between 1588 and 1595 he was bishop of Como, a diocese which included Valtellina and Valposchiavo, then both under the political control of the Three Leagues - in these Alpine borderlands with the Protestant world, Ninguarda tried to stop the spread of Protestantism.The reports from his apostolic visits to these towns in summer 1589 are historically important - they were the first apostolic visits by a Catholic bishop after a ban of many years by the Swiss authorities and the reports describe the parishes' and churches' states, the situation in other countries, the names of some priests and the numbers of Protestant residents and also include several theological and pastoral publications.On 13 June 1580 Gregory made him governor of the diocese of Regensburg, who bishop Philipp of Bavaria was still in his minority - he had been papal visitor to that diocese since 1574.