After this measure, the fiscal of the Council of the Inquisition accused the Council of Castile; he demanded that the tribunal should procure the copies and the minutes of the consultation addressed to the king; that the condemnation of it should be published, and the authors should be proceeded against. The council of the holy office, intending to act according to circumstances, represented all that had passed to the king, referring to the judgment of the theologians. The king, with the carelessness which was natural to him, merely told the inquisitor-general that he had failed in his duty, in approving a proceeding so contrary to the honour and dignity of the senate of the nation. The effects of the obstinacy and violence of the inquisitors was felt for some time after. In 1643, the king obliged Don Antonio de Sotomayor to give in his resignation.
In America, the ordinances of the king, and other regulations, could not prevent violent quarrels from arising between the civil tribunals and those of the holy office. But in all these affairs the viceroys showed more firmness, and repressed the arrogance of the inquisitors with more success than was displayed in the Peninsula. This is not surprising, because in distant countries the inquisitors are not supported by an inquisitor-general, who, possessing the king's favour, may influence him in private conversations. Besides this, the viceroys, jealous of the power with which they are invested, are careful that it shall meet with no obstacles or contradictions.
In 1686, a quarrel arose between the inquisitors of Carthagena in America, and the bishop. The inquisitor Don Francis Barela, after excommunicating the prelate, caused his decree to be read in all the churches. The bishop replied, and showed by his manner to the inquisitor, his contempt for the excommunication. Don Francis (in concurrence with his consultors) arrested and threw into prison the bishop and many respectable persons of the cathedral and the city, who had spoken freely on the subject. The Pope being informed of this affair on the 13th February, 1687, commanded the inquisitor-general, Don Diego Sarmiento de Valladares, to cause the inquisitor Barela and the consultors to be brought to Madrid, and to deprive them of their offices. This order not being obeyed, on the 15th of December he expedited a second brief, which was comminatory. The inquisitor-general then had recourse to the king, and gave so unfaithful an account of the transaction, that neither his majesty nor the council of the Indies were ever informed of the truth. The Pope persisted in his resolution, and wished to decide on the affair himself. It was not finished when Clement XI. ascended the pontifical throne; this Pope assembled the cardinals, and taking their opinions, confirmed by a formal decree all that the bishop had done, and annulled the extravagant measures of the inquisitor. A bull, in 1706, commanded the restitution of the penalties which had been imposed, and suppressed the tribunal of Carthagena. This suppression was not executed, because it was contrary to the king's policy.
In 1713, the Cardinal Francis Judice, inquisitor-general, prohibited a work of Don Melchior Macanaz, procurator of the king in the Council of Castile: the cardinal knew that this work had been printed by the order of Philip V., who had approved it after having read it. The king was at first very much irritated at this proceeding; but the cardinal, accustomed to the intrigues of Rome and Paris, succeeded in eluding the orders of his sovereign; although he was not in the kingdom, he continued to exercise his office, and sent orders to his creatures which were extremely displeasing to Philip. This prince could not obtain the dismission of Judice, until Cardinal Alberoni had exerted his influence at Rome and Paris, to second his master's views. Judice retired in 1716.
Don Melchior Macanaz continued to live in exile. His trial became important, from the great number of denunciations which were made against different works which he had written: in some of these he inveighed against the abuses which were committed at the Court of Rome, against those of the immunities of the clergy and of the ecclesiastical tribunals, and called the public attention to the fatal effects of increasing the number of monks and other societies. The qualifiers, in judging his works, clearly showed the spirit of hatred and revenge which actuated them. In the trial of Macanaz, one of his works, called A Critical Defence of the Inquisition, is mentioned; the inquisitors qualified it as ironical, because they found some things in it which were not true. They were confirmed in their opinion some time after, by another work of Macanaz, called An Apology for the Defence of Fray Nicolas Jesus de Belando, in Favour of the Civil History of Spain, unjustly prohibited by the Inquisition.
Although the inquisitors treated him with so much severity, Ferdinand VI., and the inquisitor-general Don Manuel Quintano Bonifaz, permitted Macanaz to return to Spain, and the king sent him to Aix-la-Chapelle as his ambassador.
In 1768, the inquisitors endeavoured to obtain the right of trying persons for polygamy: Charles III. ordered that the cognizance of this offence should belong to the secular judge, except when the criminals thought that it was permitted. It was his pleasure that the inquisitors "should only punish heresy and apostasy, and, above all, that none of his people should be subjected to the disgrace of an arrest, if they had not been previously convicted of a crime."
In 1771, the Council of the Inquisition represented to the king, that the simple fact of marrying another person, while the first wife was alive, was sufficient to create a suspicion that the persons guilty of it erred in faith on the article of marriage. For this reason the inquisitors continued to receive the denunciations on this pretended heresy, and to take cognizance of it.
In 1781, the inquisitor-general commanded that the confessionals in the convents of nuns should be placed within sight of the persons in the churches. This was done by the inquisitors, without consulting the archbishops and bishops of the dioceses; they were extremely offended at this conduct, but dissembled their anger, that the public tranquillity might not be disturbed.
In 1797, the Inquisitors of Grenada removed the confessional of the convent of the nuns of St. Paul, which was under the immediate direction of the archbishop: the ecclesiastical governor of the archbishopric complained to the king. The minister of justice, Don Gaspar Melchior de Jovellanos, resolved to take advantage of this event; he addressed himself to the Archbishop of Burgos, inquisitor-general, to the Bishops of Huesca, Tuy, Placentia, Osma, Avila, and to Don Joseph Espiga, the king's almoner, and requested them to propose "whatever they thought most proper to correct the abuses committed in the holy office, and to destroy the false principles on which that tribunal founded all its measures." The archbishop (as may be supposed) sent notes favourable to the tribunal; those of all the others were of quite an opposite nature. This attempt, however, did not lead to any satisfactory result: Jovellanos quitted the ministry before Charles IV. had decided on the subject; the minister who succeeded him had other views, and Jovellanos was denounced on suspicion of heresy.