Menocchio was reported to the Inquisition for the second time by Lunardo Simon, a local violinist who met the miller at a festival. Lunardo recalled that Menocchio had conveyed to him a belief in universal religious tolerance. At this point, the Inquisition resumed their investigations of Menocchio and discovered several things that concerned them: He had significant debts, his family had bullied the prior priest for reporting Menocchio to the Inquisition, to the point where the priest left town, and that he was hiding his habitello underneath outer layers of clothing. Despite their suspicion, supportive testimony by the new town priest forced inquisitors to refrain from pressing charges.

Around the same time, Menocchio encountered a converted Jew named Simon who asked him for temporary shelter. Simon reported having similar conversations with Menocchio as Lunardo had with him; he alleged that Menocchio had read the Koran and that he claimed to be associated with unspecified Lutherans. At this point, Ginzburg speculates that Menocchio felt no incentive to repress his ideas any longer, following the death of his wife and closest son. He seemed to be aware that the Inquisition would eventually prosecute and kill him (96).