There were two types of Inquisition; the ecclesiastical and the Spanish Inquisition, which were fundamentally different from each other.
A. The ecclesiastical Inquisition (investigatory or examining committee, court) was the Church's institution against heretics to oversee the purity and unity of Christian doctrine, to unveil the schemes of those who would disrupt religious unity and church discipline, and to protect the misled from being led astray. This institution was founded based on a decree issued in 1184 by Pope Lucius in agreement with Frederick Barbarossa against the Albigensians; its main operational areas were southern France and northern Italy; its goal was to root out remnants of heresies dangerous to both the Church and the state (Waldensians, Cathars, Albigensians), to win them over, or to neutralize the stubborn ones.
Later, the ecclesiastical Inquisition targeted any heresy; it naturally did not apply to Jews unless it concerned baptized Jews who relapsed, as such individuals were treated as heretical Judaizers, just as apostate Christians who converted to Judaism.
These ecclesiastical inquisitional institutions were under the direct jurisdiction of bishops, thus they were episcopal investigatory seats, with a codified procedure. Pope Innocent IV in 1248 entrusted the Dominican Order with the ecclesiastical inquisitional authority over heresies. Just as the episcopal, so too the Dominican Inquisition spread across European states: beyond Spain, Portugal, and Italy, it reached France, Germany, Hungary, Poland, and later England, wherever there was a desire to defend against dangerous heretics. However, European rulers later began using the Inquisition not to preserve the unity of faith but rather to secure their own power.
In dealing with ordinary heretics (Gottschalk, Abelard, Gilbert, Berengar, etc.), the ecclesiastical Inquisition's proceedings were mild; it aimed to neutralize them to the faithful through excommunication, at most imprisonment. However, if their teaching and attacks also aimed at subverting the ecclesiastical and social order, and if they did not cease their heresy but stubbornly clung to it, being found guilty not just against the faith but also against state laws, they were handed over to the secular authority, which typically punished such individuals with death by fire (burning at the stake) and confiscated their property. The Church itself never used physical punishments, especially not the death penalty. In interrogations, although the popes prohibited it, torture was sometimes used, following the disapproved practice and procedural model of that era's secular courts, but much less frequently and much more mildly than those courts, always considering the individual's constitution and the nature of the offense.
For what our more refined understanding and more humane sentiments may disapprove of in the Inquisition's proceedings, it is not the Church but the era that should be held responsible. Moreover, we must not forget that preserving the unity of faith and the Christian social order against disruptive elements, dangerous fanatics, and deliberate wrongdoers demanded stern and effective measures in those harsh times; the heresies that called the (ecclesiastical) Inquisition into existence threatened the very foundations of family, state, marriage, private property, and society itself, and if they had prevailed, culture would have been destroyed, and humanity would have regressed into barbarism after 600 years of the Church's sacrificial labor.
The institution of the ecclesiastical Inquisition was reorganized by Pope Paul III in 1542, and Pope Sixtus V abolished it in 1587, replacing it with the Congregatio Romanae et universalis Inquisitionis Sancti Officii (Holy Office), a church committee attentive to the purity of faith, composed of cardinals and distinguished theologians, alongside several ecclesiastical and secular legal scholars.
B. The Spanish Inquisition was established by the Spanish state power under Catholic Monarchs Ferdinand and Isabella towards the end of the 15th century (1480), primarily operating in Spain. Its goal was to preserve Spanish national and religious unity by subduing elements dangerous to the state, namely the uncontrollable Maranos (secret Jews) and later the Moriscos (secret Muslims), who mocked Christianity.
It is a great misconception or a result of malicious intent to claim that the primary purpose of the Spanish Inquisition was the confiscation of Jewish property, which was then shared between the crown and the church. Its primary and foremost goal was the protection of Christianity and the Spanish nationality against the engulfing Maranos, or the secret Judaism hiding under a Christian guise.
The Spanish Inquisition, although retaining the external forms of the ecclesiastical Inquisition, was not a church but a secular, state, political institution. Its inquisitors, whether clerical or lay, were appointed by the king, who also dismissed them from their positions, provided their remuneration, and issued instructions; they exercised their power — even if they were priests — not as the Church, but as the state, the king's officials, and executed judgments in his name.
However, this institution, originally established for racial protection purposes, increasingly became a precursor to royal absolutism against the nobility and clergy.
In his historical work, the Jewish author Grätz, discussing the Spanish Inquisition from his own Jewish bias, calls Isabella "bigoted" and zealously claims that she and Ferdinand, by establishing the Inquisition, paved the way for Spain's impoverishment and decline. (Geschichte der Juden, V. Bd. Leipzig, 1864. pp. 300—363.) However, he is mistaken, as Spain's subsequent decline was caused by other factors.
Undeniably, Ferdinand, with the Spanish Inquisition, not only created national and religious unity but, as the Inquisition later primarily aimed to prevent the infiltration of Protestantism starting with Martin Luther (1483—1546), saved Spain from the schism that, at the beginning of the modern era, brought bloody civil wars to other European countries.
The Spanish Inquisition worked with extremely harsh means (prolonged investigative imprisonment, torture, life imprisonment, death by burning).
The Spanish Inquisition cannot and should not be attributed to the Church, as the popes protested against this state institution, often raising their voices against its excessive harshness and, especially initially, severe abuses.
The Spanish Inquisition was abolished only in 1820, after about two and a half centuries of operation. It was briefly revived later but was permanently abolished by the council of state in 1834. In Portugal, the Inquisition was dissolved in 1821.
When attacking the Inquisition, it is usually the Spanish Inquisition that is meant, as the anti-Inquisition accusations typically refer specifically to it. However, even with the Spanish Inquisition, the following should not be overlooked:
a) Primarily, that the main goal of the Spanish Inquisition was originally to investigate the dealings of Maranos and Moriscos (apparently converted Moors) who were conspiring against Christian Spain and plotting multiple uprisings. This was not directly a religious matter but one of state security. In the centuries-long defensive struggle that Spanish Christianity waged against its sworn enemies, the Moors and Jews, the Inquisition was the last weapon of the Christian national kingdom against the overconfident (secret) Jewry aiming to subject all of Spain under Jewish rule, and the Moors (Moriscos) counting on the support of their African co-religionists and the Turks to re-establish the old Moorish rule. The Spaniards, who had suffered under Moorish rule for nearly 800 years, dreaded its return and the subsequent subjugation of Spain.
b) The jurisprudence of the 15th century was merciless, even cruel, worldwide; however, despite its strictness, the prosecutorial process of the Spanish Inquisition was much more humane and milder than that of all other secular, state courts of the era. The Inquisition exercised much greater caution in the use of torture compared to the courts of other countries. Only with special permission from the chief inquisitor and always in the presence of a supervising physician could physical punishment be applied; over time, the original severity lessened; from 1500 onwards, the repeated use of torture was strictly forbidden. The reason the Middle Ages used torture (torture for confession) is that the medieval justice system believed that the queen of evidence (regina probationum) was not the testimony of witnesses but the confession. — Death by fire (burning at the stake) was not a punishment exclusive to heretics, but in the 15th and 16th centuries, it was a special punitive tool for those who offended the divine Majesty.
The prisons of the Inquisition were also different from the prisons of that era; they were well-arched, bright, and dry rooms where the prisoner was not shackled and could move around. The provision of food was much better than in other prisons. Special care was given to the sick prisoners. The Inquisition's representatives occasionally inquired whether the supervisors and guards were treating the prisoners well.
The auto-da-fé was not the burning of the condemned, as sensationalist historians and novelists narrate. The Spanish word fé (faith) should not be confused with the French feu (fire). The auto-da-fé, in Latin: actus fidei (= act of faith, deed of faith) was a religious act, either the release of the innocent or the reconciliation of the repentant sinner with the Church, symbolized by holding a burning candle in hand as a sign of their revived faith, making a confession of faith (actus fidei) and renouncing heretical doctrines, accompanied by an exhortatory sermon.
The immuratio (from the Latin murus = wall) was not "being walled alive" as some novelists who do not understand medieval Latin think, but imprisonment; placing the individual in solitary confinement (“between four walls”).
The sanbenito or sacbenito (from Latin: saccus benedictus; Spanish: sacco bendito = blessed sack) was neither a "straitjacket" nor a "mocking cloak," but a type of robe made of coarse, yellowish-brown linen, consecrated by the church for penance. Many medieval rulers also donned such garments towards the end of their lives in preparation for death. Those absolved by the Inquisition were required to wear this for a certain period. The garments of the obstinate heretics handed over to the secular authority for execution typically had flames and images of the devil painted on them.
c) The victims of the Inquisition were not all punished for their faith or lack thereof (heresy); under Torquemada's inquisitorship, the Spanish Inquisition dealt not only with religious offenses but also a whole range of other moral crimes and civil, political felonies: blasphemy, polygamy (imported from the Moors), fornication, sodomy, church pillaging, espionage, treason, rebellion, murder, smuggling, usury, witchcraft, and the "witch trials."
d) Like all human institutions, the Spanish Inquisition also had its abuses. It is undeniable that the Spanish Inquisition often treated the accused with excessive harshness; it is also undeniable that the number of its victims was not insignificant. (According to Gams, III, 2. p. 74, the number of those executed for heresy was about 4000.) However, it is also undeniable that biased and deliberately falsifying historiography, mainly by anti-church historians who wish to hold the Church responsible for the errors of the Spanish Inquisition, unscrupulously embellish its cruelties and unjustly exaggerate the number of its victims, especially based on the biased work "Histoire critique de l’inquisition d'Espagne" (Paris, 1817—1818) by Juan Antonio Llorente (1756—1823), a Spanish apostate canon and free-thinking writer who was forced to flee to France due to treason but was later also expelled from there. Llorente, the "homo mendax," had his exaggerations and distortions recently refuted by the Protestant Schäfer ("Beiträge zur Geschichte des spanischen Protestantismus und der Inquisition des 16. Jahrhunderts, 1902. 3 volumes). Nonetheless, due to the biased falsifications of anti-church historians, the horror stories told about the Spanish Inquisition are ineradicable from pulp fiction novels.
e) The inquisitors, accused of religious intolerance, were no more tolerant towards Catholics than the so-called reformers of the 16th and 17th centuries, nor did they respect "freedom of conscience" any more. In fact, they practiced the Protestant principle of "cuius regio, eius religio" (the religion of the ruler is the religion of the state) — which gained ground through its enforcement — with even less tolerance and more cruelty towards Catholics than the Inquisition. (Zwingli, Calvin, Henry VIII, Edward VI, Elizabeth, etc.)
f) Even if we were to believe all the exaggerations that anti-church writers like to tell, it is certain that during the entire duration of the Inquisition's operation, not as many people fell victim as in just one of those countries where Protestantism was introduced by force of arms, such as England, the Netherlands, Scandinavia, Ireland, etc., where thousands of Catholics loyal to their faith and the Pope were murdered. What is the Spanish Inquisition compared to the martyrs of Protestant intolerance!?... Compared to the horrors of the Protestant investigative courts and blood courts, the Spanish Inquisition was — an innocent matter... And yet, although these facts are well known and not even denied by objective Protestant historians, — they are usually silenced, and the horrors of the Spanish Inquisition are shamelessly blamed on the Catholic Church (!).
g) The enemies of the Church, in order to create sentiment against the Church, either out of ignorance or malice, attribute the severity of the Spanish Inquisition to the Church, whereas it was precisely the Popes (Sixtus IV, Leo X, Gregory XIII, Paul III) who repeatedly protested against the Spanish Inquisition as applied by the Spanish kings, and even wanted to abolish or at least reform the entire institution. They repeatedly excommunicated abusive inquisitors, constantly admonished the judges to moderation, but their decrees were embezzled or their proclamations were prevented by the kings.
h) The Church has never converted, nor does it convert by force, because its principal stance is that no one should be compelled to embrace the Catholic faith against their will. ("Ad amplexandam fidem catholicam nemo invitus cogatur". CIC. can. 1351.), and that the purity of faith should be preserved solely by spiritual means. (Forced conversions have never redounded to the glory of the Church, neither under the rule of the Visigoths nor in later times with forced baptisms.) Therefore, the Church has always disapproved of religious coercion originating from the state, as practiced by the Inquisition, whose legitimacy it can never recognize. This is why, no matter how useful the Inquisition was to Spain, the Popes always disapproved and condemned its acts of violence and every single act of cruelty.