Rodrigo de Valero told Egidius that the books from which he derived his knowledge were worth nothing, and that his preaching would never be admired, if he did not study the Bible. Egidius took his advice, and in time acquired a style of preaching extremely agreeable to the people, but his success raised him many enemies.

The emperor gave him the Bishopric of Tortosa in 1550, which increasing the envy and hatred of his enemies, they denounced him to the Inquisition of Seville as a Lutheran heretic, for some propositions which he had advanced in his sermons, and which they separated from the other parts, to give them a different sense from what they would otherwise have had; they took advantage of the favour he showed to Rodrigo Valero in 1540 during his trial, and of some other circumstances, to injure him.

Egidius was taken to the secret prisons of the holy office in 1550: he made use of this opportunity to compose his apology, which rendered the storm his enemies had raised still more violent. His simplicity had made him, in his apology, establish as certain principles, some propositions which the scholastic theologians looked upon as erroneous, and tending to heresy. The conduct and morals of Egidius were so pure, that the emperor wrote in his favour, the chapter of Seville followed his example, and (what is still more remarkable) the licentiate, Correa, Dean of the inquisitors, was touched by his innocence, and undertook to defend him against his colleague, Pedro Diaz, who bore the greatest hatred to the accused. This circumstance was particularly mortifying to Egidius, as his enemy formerly held the same opinions, and had likewise studied in the school of Rodrigo Valero.

The interest which Egidius had inspired induced the inquisitors to accede to his proposal of a discussion between him and some learned theologians. Brother Garcia de Arias, of the convent of St. Isidore of Seville, was chosen; but his opinion was not deemed sufficient, and Juan Gil demanded the Dominican friar, Dominic Soto, should be summoned to the conference. This incidence retarded the trial, but Soto at last arrived at Seville.

According to Gonzales de Montes, this theologian held the same opinions as Egidius; but to prevent the suspicions which might arise from this circumstance, he persuaded Egidius to draw up a sort of confession of faith. They agreed that both should write their opinions, and only communicate them to each other in public. This author states that these confessions of faith were compared, and found to accord perfectly.

The inquisitors being informed of this arrangement, declared that, as the reputation of a bishop was concerned, it was necessary to convoke a public assembly, where Dominic Soto should explain the object of the meeting in a sermon, and read his confession of faith; that Egidius should afterwards read his, that the assembly might judge of the conformity of their opinions. The inquisitors caused two pulpits to be prepared, but, either by chance, or from a private order, they were so far apart, that Egidius could not hear what Soto said.

Soto[12] read an exposition of his principles entirely different from that on which they had agreed in their private conferences; and as Egidius did not hear him, and supposed that he was reading the same confession which he had approved, he consequently made signs with his head and hands that be accorded with his propositions. Egidius then began to read his confession of faith, but those who understood the subject, soon perceived that there was not the slightest resemblance between them, and that Egidius held several opinions entirely opposite to some propositions advanced by Dominic Soto, and acknowledged as dogmatical by the tribunal of the faith: this circumstance effaced the favourable impressions produced by the gestures of Egidius. The inquisitors added these writings to those of the trial, and passed judgment upon Egidius according to the advice of Soto. He was declared violently suspected of the Lutheran heresy, and condemned to three years' imprisonment; he was prohibited from preaching, writing, or explaining theology for the space of ten years, and never to leave the kingdom on pain of being considered and punished as a formal heretic.

Egidius remained in prison until 1555; he was at first extremely astonished at his situation, after having perfectly agreed with the Dominican on all the points in question. He was not undeceived, until some of his fellow-prisoners informed him of the difference of his articles with those of Soto, and the treachery of that monk.

Egidius took advantage of the short interval of liberty which followed his imprisonment to go to Valladolid, where he had an interview with Doctor Cazalla and other Lutherans in that city: on his return to Seville he fell sick, and died in 1556. The tribunal being informed of his intercourse with heretics, instituted another trial, and pronounced that he died an heretic; his body was disinterred, and burnt with his effigy, in a solemn auto-da-fé, his memory declared infamous, and his property confiscated: this sentence was executed in 1560.

It will be necessary here to quote a letter of Don Bartholomew Carranza to Brother Louis de la Cruz, a Dominican, and his disciple. The archbishop mentions as a well-known circumstance, that his catechism had been presented to the holy office; Brother Melchior Cano and Dominic Soto had been commissioned to censure it, and that they had judged unfavourably of his work. He complained much of this conduct in Soto; he said he could not comprehend such scruples in a man who had been so indulgent to the Doctor Egidius who was considered as an heretic, while, on the contrary, the author of the Catechism had combated the opinions of the heretics of England and Flanders; that Soto had judged the book of a Dominican monk no less favourably, while he treated an archbishop, whom he was bound to respect, without consideration; that he would, in consequence, write to Rome and Flanders, where he hoped that his propositions would be more favourably received than at Valladolid; but that, at all events, Pedro de Soto, confessor to the emperor, would write to Dominic, and he hoped that the Almighty would allay the tempest which had been raised around him.