When the king had given his consent that the archbishop should be prosecuted, he required that he should be treated with the respect due to his dignity: this he repeated in a letter to Cardinal Pacheco, who informed him that Carranza had demanded that his affair should be judged at Rome. The king also wrote two letters to Carranza on the 30th of March, and the 4th April, in which he promised to protect him. The letter to Cardinal Pacheco induced the grand-inquisitor to write to the king on the 19th of May, when he informed him of the measure which had been decreed, adding, that he thought a citation to appear more moderate, less humiliating, and more private than an arrest by alguazils. The king, however, had still some regard for Carranza, since he did not approve of what had been done. At this period Don Antonio de Toledo, who continued to correspond with Carranza, informed him, that though he did not think the affair had taken so favourable a turn as might be wished, yet he thought he still perceived some marks of attachment for him in the king, in spite of the evil report made of him.
At last, on the 26th of June, the king sent an answer to the inquisitor-general, in which he gives his consent to what had been resolved upon; adding, that he hoped the execution of this measure would be attended with all the consideration due to the merit of Carranza, and the dignity with which he was invested. The prelate was informed of this event, in a letter written by Don Antonio de Toledo, the next day. The approbation of the king was received on the 10th of July, and on the 15th the fiscal presented a second requisition, in which he insisted on the execution of the demand contained in the first, that Carranza should be arrested, and his goods seized. He represented that the instruction of the process furnished proofs which ought to have been considered sufficient on the 13th of May; that nevertheless he would add to them the deposition of Donna Louisa de Mendoza, wife of Don Juan Vasquez de Molina, secretary to the king. This lady deposed, that the Marchioness d'Alcañices told her, that, according to the instructions of the archbishop, it was not meritorious in the sight of God to deprive ourselves of pleasures, and that it was not necessary to wear haircloth. The marchioness, who was examined, declared that she had never said anything of the kind, but only that all these things were less meritorious; that she had been intimate with the archbishop for more than twenty years, and had been his penitent, but during all that time she had never heard him say any thing against the faith.
On the 1st of August, the grand-inquisitor, in concert with the Supreme Council, and several consultors, issued the order for the arrest of the archbishop. At this juncture, Philip II. wrote to his sister, the governess of the kingdom, saying, that in order to avoid the scandal and inconveniences arising from the measures decreed by the holy office, it would be proper to send for the archbishop to court upon some decent pretext. Don Antonio de Toledo having heard some hints of this, hastened to communicate it to Carranza, on the 19th of July: this was the last letter that faithful friend wrote to him. Among the papers of the archbishop, were found letters from persons, who afterwards, from want of courage, joined his enemies. There was also found the minutes of a representation in Latin, addressed to the Pope, in the name of the chapter of Toledo, entreating his holiness not to allow the cause of Carranza to be judged by the holy office of Spain, alleging that its members were swayed by human motives, and not from zeal to religion: it is not certain if this petition reached the Court of Rome, but the chapter behaved to the prelate with great generosity.
The regent wrote a letter to the archbishop on the 3rd of August, in which she says, that before the arrival of the king, which would soon take place, she wished to communicate some affairs to him, and therefore begged him to repair immediately to Valladolid, adding, that as the least delay might occasion very disagreeable consequences, she should be pleased if he came as soon as possible, even if without ceremony or equipage, and that she sent Don Rodrigo de Castro that he might not lose time, and might inform her of his arrival.
This Don Rodrigo de Castro was the nephew of the Bishop of Cuença, the first denouncer of Carranza: he departed from Valladolid on the 4th of August; on the 6th he delivered the letter to the archbishop, who, on the next day, replied to the princess that he would obey her orders. He immediately sent his equipages and part of his household to Valladolid, but followed slowly, that he might visit the towns and villages of his diocese, which he was to pass through.
During this interval, Don Rodrigo wrote several letters to Valdés, one dated the 4th of August, from Arevalo, and four from Alcala de Henares, dated the 7th, 9th, 10th, and 14th, from which the inquisitor-general concluded that the delay of eight days was too long, and concealed some bad design: he pretended to think that Carranza intended to make his escape to Rome, yet Don Rodrigo de Castro lodged in the same house, and never lost sight of him. This pretext, futile as it was, gave Valdés the opportunity of issuing a mandate on the 17th, appointing Don Rodrigo and Don Diego Ramirez de Sedeño inquisitors of the districts of Toledo and Valladolid. He commissioned them and the chief alguazil of Valladolid to seize the person of the archbishop, to sequestrate his goods, and draw up an inventory of them.
This order was executed at Torre-Laguna, on the 22nd, before day, and while the archbishop was still in bed. When he was told that he was under arrest, he demanded to know by whose order he was made prisoner; that of the inquisitor-general, and the brief of the Pope, were shown to him. He replied that the brief was general, and that it ought to be a special commission expedited with a knowledge of the cause, which was out of the jurisdiction of the inquisitor-general: that even supposing him to be competent, the conditions prescribed in the brief were not observed in his case, since nothing but malice could inspire the fear that he should attempt to escape; that, from all these considerations, he protested against the order of the grand-inquisitor, and the violence of his measures, and demanded satisfaction of the Pope for the insult he had received. Not being able at that moment to put his intentions into execution, the archbishop desired Juan de Ledesma, the notary of the holy office, who was present at his arrest, to write down his replies to the inquisitors, and that he obeyed the order only to avoid ill-treatment.
The archbishop requested that great care might be taken of his papers, some of which belonged to trials concerning the archiepiscopal see, and were of great importance. All that he requested was complied with on this subject.
On the 23rd of August he left Torre-Laguna, and arrived at Valladolid on the 28th; he was imprisoned in the house of Don Pedro Gonzalez de Leon: his portfolio, and a box containing papers, were sent to the inquisitor-general, who immediately caused them to be opened, and an inventory taken of their contents. On the 6th of September he addressed a letter to the king, giving an account, in his manner, of the arrest, and alleging his pretended fear of the flight of Carranza, as the motive for it. He added, that the archbishop appeared to be informed of his proceedings; an insinuation which might have injured Don Antonio de Toledo, whose correspondence he had read.