The impact of the Protestant Reformation and Catholic Reform movement on the ecclesiastical censorship of science, philosophy and magic has been an enduring theme in the historiography of early modern Italy. In this paper, I consider how the Church’s desire to defend the truth of miracles from Protestant criticisms on the one hand and their efforts to centralise the process of verifying miracles on the other affected the investigation of philosophical works. Taking the case of Girolamo Cardano, whose works were the subject of intensive investigation by the Catholic Church from the 1570s, I examine the issues that censors flagged as points of concern. One recurring theme was the fact that his accounts of the cosmos appeared to offer natural explanations for miracles and the actions of the martyrs. Although the intellectual problems raised by Cardano’s work were far from new, I suggest that the events of the sixteenth century raised their salience with Church authorities.