The Inquisition was established in 1478 by Catholic Monarchs Ferdinand of Aragon and Isabella of Castile to maintain Catholic orthodoxy in their kingdoms and was under the direct control of the Spanish monarchy. It was not definitively abolished until 1834, during the reign of Isabel II. The Inquisition, as an ecclesiastical tribunal, had jurisdiction only over baptized Christians. However, since Jews (in 1492) and Muslim Moors (in 1502) had been banished from Spain, jurisdiction of the Inquisition during a large part of its history extended in practice to all royal subjects. The Inquisition worked in large part to ensure the orthodoxy of recent converts known as conversos or marranos.

During the period in office of Diego Deza (1499–1507), the successor of Torquemada as grand inquisitor, himself of Jewish blood, the excesses committed – in particular by Diego Rodríguez Lucero, the inquisitor of Córdoba – were notorious: accusations were made wholesale on the flimsiest grounds; incredible cruelties were perpetrated; and no accused person had any chance to escape. The culmination was reached when no less than 107 persons were burned alive on an accusation of having listened to the preaching of one Membreque, a bachelor of divinity. Complaints against these atrocities became so widespread that on Sept. 30, 1505 Philip and Juana suspended the action of the Inquisition in Castile until they returned from Flanders. However, the death of Philip put an end to this plan, and Lucero was emboldened to issue another wholesale batch of accusations, including one against the saintly Hernando de Talavera – archbishop of Granada and formerly confessor to Isabella the Catholic herself – who died in consequence of the humiliation imposed upon him. The popular outcry now led Ferdinand to dismiss Deza and to appoint Cardinal Ximénes de Cisneros in his place as grand inquisitor (1507). Proceedings instituted against Lucero were allowed to drop. On the accession of Charles V, the Spanish New Christians sent him promises of enormous sums if he would restrict the power of the Inquisition in his dominions and abolish secret accusations. Similar steps were taken at Rome, where Pope Leo X prepared a bull in the sense desired. Charles, however, after temporary vacillation, displayed the narrow obscurantism which was to characterize him through life, and effectively prevented the publication of the bull. Thereafter, there was no serious challenge to the authority of the Inquisition in Spain and it could count throughout upon royal support. Charles' son, Philip II, carried on and enhanced his father's obscurantist tradition, maintaining the tribunal in all of its terrible power in spite of the protests of the Cortes. Under Philip III, the conde-duque de Olivares endeavored to restrict its might; but on his fall it continued with its influence if anything increased. It was under this king and his successor, Philip IV, that the tribunal attained its greatest power and pomp.

The number of the Spanish tribunals ultimately totaled 15: Barcelona, Córdoba, Cuenca, Granada, Logroño, Llerena, Madrid (called also Corte), Murcia, Santiago, Seville, Toledo, Valencia, Valladolid, and Saragossa, and Palma (Majorca). All acted under the authority of the central tribunal (the "supreme"). Activity, as far as Judaizers were concerned, was greatest in Old Castile and least in Catalonia. As time advanced, however, the exclusive preoccupation of the Inquisition with the New Christians came to be qualified. From 1525, Moors faithful to the religion of their fathers also fell within its scope, and as the century advanced, there was an increasing number of Protestants and Alumbrados, or visionaries. By the middle of the 16th century, indeed, the native tradition of crypto-Judaism had to a large extent become extirpated, owing to the incredible severity of the Inquisition in the first years of its existence. However, the place of the Spanish Judaizers was taken, especially during the period of the union of the two countries, by immigrants from Portugal, or else their immediate descendants. At the beginning of the 18th century, with the less obscurantist era which dawned with the house of Bourbon, there was some slight mitigation, particularly as far as the Judaizers were concerned, but in 1720 the discovery of a secret synagogue in Madrid led to a considerable recrudescence of activity throughout the country. During the reign of Philip V (1700–46), 1,564 heretics were burned and 11,730 reconciled to the Church, a good proportion for Judaizing. After this outburst, the activity of the Inquisition gradually diminished, though more through lack of material than through any diminution of zeal.

It is estimated that in Spain, from the establishment of the Inquisition down to 1808, the number of heretics burned in person was 31,912; those burned in effigy, 17,659; and those reconciled de vehementi (see Procedure, below), 291,450 – a total of 341,021 in all. Even these immense figures are apparently exceeded by the usually careful Amador de los Rios, who estimates that up to 1525, when the Moriscos first Page began to suffer, the number of those burned in person came to 28,540; those burned in effigy to 16,520; and those penanced to 303,847 – making a total of 348,907 condemnations for Judaism in less than half a century. On the other hand, Rodrigo, the apologist of the Inquisition, puts forward the impossible assertion that less than 400 persons were burned in the whole course of the existence of the Inquisition in Spain. It was in the earlier and most ferocious period of inquisitional activity that the secret Jews suffered above all, and they furnished therefore a disproportionate number of the victims. In the later period, the number greatly diminished. Thus, from 1780 to 1820, out of 5,000 cases, only 16 were of Judaizing; but the majority of the charges at this period were light, and the sentences imposed in most cases comparatively negligible.