Although the Indigenous people were originally subject to the jurisdiction of the inquisitors, they were eventually removed from the control and not seen as fully responsible for deviation from faith. They were still subject to trial and punishment by the Episcopal inquisition. In the eyes of the church the Indigenous were seen as gente sin razón, individuals without reason.
As a result their trials were separate from other inquisition cases. In spite of that, it still did not stop other people that were of non-Indigenous descent from being accused of other crimes that were against the Church. These crimes could range from heresy, sorcery, witchcraft, and other superstitious practices.
People accused of these crimes were generally individuals who came from a lower status of Peruvian society. Among them were individuals of African descent, mestizos, women, and Jewish or Protestant Europeans seeking refuge from religious persecution.
In 1813 it was first abolished by virtue of a Cortes decree. In 1815 it was reconstituted but their target was now the ideas from the French Encyclopedists and similar texts, and most people who were accused of crimes were only given probation. With the promotion of Freemason José de la Serna to the viceroyship, which coincided with the rise of the nationalist faction (as both factions prepared to fight each other in the Peruvian War of Independence), the Inquisition fell apart of its own volition.
- Teodoro Hampe-Martinez, p. 43.
- Benjamin Keen and Keith Haynes, p. 106.
- Teodoro Hampe-Martinez. "Recent Work on the Inquisition and Peruvian Colonial Society,1570-1820". Latin American Research Review. Vol. 31 No.2 (1996).
- Benjamin Keen and Keith Haynes. A History of Latin America Volume 1 Ancient America to 1910. 7th Edition. New York: Houghton Mifflin Company, 2004.
- Henry C. Lea. The Inquisition in Spanish Dependencies; Sicily, Naples, Sardina, Milan, the Canaries, Mexico, Peru, New Granada. New York: The Macmillan Company, 1908.
- Cecil Roth. The Spanish Inquisition. New York: W.W. Norton & Company, 1964.
- Irene Silverblatt, Modern Inquisitions: Peru and the Colonial Origins of the Civilized World. Durham, NC: Duke University Press, 2004.
- Henry C. Lea (1829-1909): The Inquisition in 17th-Century Peru: Cases of Portuguese Judaizers from the Internet Modern Sourcebook
- "South and Central America: Peru and Chile", from the Jewish Encyclopedia (1901).
- Museo de la Inqusición y del Congreso, located in Lima, Peru.