So far he had had to deal with the episcopal Inquisition in the hands of an opposing faction; even severer experiences were in store for him from the Holy Office, used as an instrument by the Viceroy Toledo who desired to get rid of him. One of the earliest acts of the Lima tribunal was to entertain a denunciation of him, in which his intemperate utterances were again brought forward, together with the further accusation that he had banished from Tucuman all who had been concerned in his prosecution and that he had said that he had been forced to confess to what he had not done. March 14, 1570, Cerezuela ordered his arrest with sequestration of property; Toledo undertook to execute the mandate and in reporting to the king stated that Aguirre’s government was such that most of the inhabitants were leaving the province. To arrest such a man was not an easy matter, but it was effected and he was brought three hundred leagues to Lima. Delays were unavoidable in obtaining and ratifying testimony at such a distance, through a hostile Indian country which, as the tribunal stated, was entered only once a year. Aguirre offered to waive the formality of ratifying the testimony in order to expedite the process, but the fiscal insisted on regularity and the trial dragged wearily on, as new evidence came in, mostly as to his arbitrary government and other matters with which the tribunal properly had no concern. Aguirre fell dangerously ill and was transferred, July 19, 1572, to the house of a familiar, where he was kept strictly _incomunicado_ and from which he was brought back, April 24, 1574, to listen to the publication of evidence. It was not until late in 1575 or early in 1576 that sentence was rendered condemning him to hear mass as a penitent on a feast-day when no services were allowed in any other church; he abjured _de vehementi_, was cast in all costs, was recluded for four months in a convent and was banished perpetually from Tucuman. The trivial character of the charges is seen in the special stress laid on his having used charms to cure wounds and toothache, which he was forbidden to do in future--innocent charms, as he explained, employed only because no physician was at hand and surely pardonable in the wild warfare in which he had worn out his life. He retired to the city of Serena which he had founded, old, sick and penniless. He had spent thirty-six years and some three hundred thousand pesos in the king’s service; three of his sons, his brother and three nephews had died in the same service, and he was too poor and oppressed with debts to make his way to court and ask reward for his labors. To complete the destruction of his influence his two remaining sons were prosecuted on frivolous charges, but the cases seem to have been suspended after the desired result had been attained. His son-in-law, Francisco de Matienzo, who had endeavored to prevent his arrest, was prosecuted and fined in three hundred pesos.