Though the new approbation given to Molinos' book by the inquisition had checked the proceedings of his enemies; yet they were still inveterate against him in their hearts, and determined if possible to ruin him. They insinuated that he had ill designs, and was, in his heart, an enemy to the Christian religion: that under pretence of raising men to a sublime strain of devotion, he intended to erase from their minds a sense of the mysteries of christianity. And because he was a Spaniard, they gave out that he was descended from a Jewish or Mahometan race, and that he might carry in his blood, or in his first education, some seeds of those religions which he had since cultivated with no less art than zeal. This last calumny gained but little credit at Rome, though it was said an order was sent to examine the registers of the place where Molinos was baptised.
Molinos finding himself attacked with great vigour, and the most unrelenting malice, took every necessary precaution to prevent these imputations being credited. He wrote a treatise, entitled Frequent and Daily Communion, which was likewise approved by some of the most learned of the Romish clergy. This was printed with his Spiritual Guide, in the year 1675; and in the preface to it he declared, that he had not written it with any design to engage himself in matters of controversy, but that it was drawn from him by the earnest solicitations of many pious people.
The Jesuits, failing, in their attempts of crushing Molinos' power in Rome, applied to the court of France, when, in a short time, they so far succeeded, that an order was sent to cardinal d'Estrees, commanding him to prosecute Molinos with all possible rigour. The cardinal, though so strongly attached to Molinos, resolved to sacrifice all that is sacred in friendship to the will of his master. Finding, however, there was not sufficient matter for an accusation against him, he determined to supply that defect himself. He, therefore, went to the inquisitors, and informed them of several particulars, not only relative to Molinos, but also Petrucci, both of whom, together with several of their friends, were put into the inquisition.
When they were brought before the inquisitors, (which was the beginning of the year 1684) Petrucci answered the respective questions put to him with so much judgment and temper, that he was soon dismissed; and though Molinos' examination was much longer, it was generally expected he would have been likewise discharged: but this was not the case. Though the inquisitors had not any just accusation against him, yet they strained every nerve to find him guilty of heresy. They first objected to his holding a correspondence in different parts of Europe; but of this he was acquitted, as the matter of that correspondence could not be made criminal. They then directed their attention to some suspicious papers found in his chamber; but Molinos so clearly explained their meaning, that nothing could be made of them to his prejudice. At length, cardinal d'Estrees, after producing the order sent him by the king of France for prosecuting Molinos, said, he could prove against him more than was necessary to convince them he was guilty of heresy. To do this he perverted the meaning of some passages in Molinos' books and papers, and related many false and aggravating circumstances relative to the prisoner. He acknowledged he had lived with him under the appearance of friendship, but that it was only to discover his principles and intentions: that he had found them to be of a bad nature, and that dangerous consequences were likely to ensue; but in order to make a full discovery, he had assented to several things, which, in his heart, he detested; and that, by these means, he saw into the secrets of Molinos, but determined not to take any notice, till a proper opportunity should offer of crushing him and his followers.