He was prosecuted in 1604 by the Inquisition for atheism and the Averroist heresy of "double truth", and ordered to refute his claims: as was his manner, Cremonini gently refused to retract himself, sheltering himself behind Aristotle's authority.

As for the accusations, and beyond Cremonini's teachings: indeed his personal motto was "Intus ut libet, foris ut moris est"[13] (Latin for "In private think what you wish, in public behave as is the custom"), which was taken by humanists as meaning that a scientific thinker could hold one set of opinions as a philosopher, and another set as a Christian; it was also adopted by European Libertines (brought back to France by his student and confidant Gabriel Naudé).

His student Naudé (who had been his confidant for three months) qualified most of his Italian teachers as "Atheists"[14] and especially Cremonini as a "déniaisé" ("one who has been wised up, unfoolish, devirginized", the Libertines' word for unbelievers); he added to his friends, translated, "The Cremonin, Professor of Philosophy in Padua, confessed to a few choice Friends of his that he believed neither in God, nor in Devil, nor in the immortality of the soul: yet he was careful that his manservant was a good Catholic, for fear he said, should he believe in nothing, that he may one morning cut my throat in my bed".

[15] Later, Pierre Bayle pointed out that Cremonini did not believe in the immortality of the soul (in the "Crémonin" article of his Historical and Critical Dictionary).

[16] Pierre Larousse, in his opinionated Grand dictionnaire universel du XIXe siècle, stated Cremonini was not a Christian.

[17] Years later, in his book Dialogue Concerning the Two Chief World Systems, Galileo would include the character Simplicio - the name was not casually chosen - a dogmatic Aristotelian philosopher who was partly based on Cremonini.