The major target of the Portuguese Inquisition were those who had converted from Judaism to Catholicism, the Conversos, also known as New Christians or Marranos, who were suspected of secretly practising Judaism. Many of these were originally Spanish Jews, who had left Spain for Portugal. The number of victims is estimated around 40,000.
As in Spain, the Inquisition was subject to the authority of the King. It was headed by a Grand Inquisitor, or General Inquisitor, named by the Pope but selected by the king, always from within the royal family. The Grand Inquisitor would later nominate other inquisitors. In Portugal, the first Grand Inquisitor was Cardinal Henry, who would later become king. There were Courts of the Inquisition in Lisbon, Coimbra, and Évora, and for a short time (1541 until c. 1547) also in Porto, Tomar and Lamego.
It held its first auto-da-fé in Portugal in 1540. Like the Spanish Inquisition, it concentrated its efforts on rooting out those who had converted from other faiths (overwhelmingly Judaism) but did not adhere to the strictures of Catholic orthodoxy.
The Portuguese Inquisition expanded its scope of operations from Portugal to Portugal's colonial possessions, including Brazil, Cape Verde, and Goa, where it continued investigating and trying cases based on supposed breaches of orthodox Roman Catholicism until 1821.
King João III who requested the Inquisition in Portugal.
Under John III, the activity of the courts was extended to the censure of books, as well as undertaking cases of divination, witchcraft and bigamy. Originally aimed at religious matters, the Inquisition had an influence on almost every aspect of Portuguese life — political, cultural, and social.
One of the main targets of the Inquisition were also the Portuguese Christian traditions and movements that did not conform with the orthodoxy. The millenarian and national Feast of the Cult of the Empire of the Holy Spirit, dating from the mid 13th century and spread throughout all mainland Portugal in that century and in the 14th century, and the following centuries throughout its Atlantic islands and the empire, was the main target of prohibition and surveillance by the Inquisition after 1540s, having almost disappeared from Continental Portugal and India. The spiritual tradition, made up exclusively by non-religious officials and popular Brotherhoods in the Middle Ages and in the following centuries, was gradually restored only after the second half and late 20th century in some municipalities of mainland Portugal, although mostly, with the exception of a few faithful and accurate local traditions, still with major deletions and changes (in what remained or was restored) of the ancient rituals.
According to the traditional Feast of the Empire of the Holy Spirit, celebrated at the feast of the Pentecost, a future age - the third age, would be governed by the Empire of Holy Spirit and would represent a monastic or fraternal governance, in which the hierarchy of the Catholic Church, the intermediaries and the organized Churches would be unnecessary, and infidels would unite with Christians by free will. Until the 16th century, this was the main annual festivity in most of the Portuguese major cities, celebrating each city even more than one Feast, such as in Lisbon (with 8), Porto (4), and Coimbra (3). Obviously the orthodoxy of the Church and the Inquisition could not tolerate a spiritual tradition entirely popular and without the mediation of the clergy at the time, and most importantly, celebrating a future Age which would bring the end of the Church.
The cult of the Holy Spirit survived in the Azores Islands, held by the local population and under the traditional protection of the Order of Christ, and where the arm of the Inquisition did not extend its power so effectively, despite the surveillance made by the local ecclesiastical authorities, reporting the Feast. Beyond the Azores, the cult of the Empire of the Holy Spirit survived in many parts of Brazil (where it was established in the 16th, 17th and in the 18th centuries), being celebrated today in all its states, except two, and in pockets of Portuguese settlers in North America (Canada and U.S.A.), mainly of Azorian descent.
The movements and concepts of Sebastianism and of the Fifth Empire were therefore sometimes also target of the Inquisition (being the most intense persecution of Sebastianists during the Philippine Dynasty, lasted however beyond that period), both considered also unorthodox and sometimes entirely heretical, but by an intermittent and selective manner, since some important familiares (associated people) of the Holy Office (Inquisition) were Sebastianists.
In 1674 the Inquisition was suspended in Portugal; autos-da-fé were suspended and inquisitors were instructed not to inflict sentences of relaxation, confiscation, or perpetual galleys between 1674 and 1681, much of this by the action of António Vieira in Rome, in order to put an end to the Inquisition in Portugal and its Empire. Vieira had earned the name of the Apostle of Brazil. At the request of the pope he drew up a report of two hundred pages on the Inquisition in Portugal, with the result that after a judicial inquiry Pope Innocent XI suspended it for five years (1676–81).
António Vieira had long regarded the New Christians with compassion and had urged João IV, in which he had much influence and support, not only to abolish confiscation but to remove the distinctions between them and the Old Christians. He had made enemies and the Inquisition readily undertook his punishment; his writings in favor of the oppressed were condemned as "rash, scandalous, erroneous, savoring of heresy and well adapted to pervert the ignorant". After three years of incarceration, he was penanced in the audience-chamber of Coimbra, December 23, 1667, and his sympathy for the victims of the Holy Office was sharpened by his experience of its "unwholesome prisons, where he tells us that five unfortunates were not uncommonly placed in a cell nine feet by eleven, where the only light came from a narrow opening near the ceiling, where the vessels were changed only once a week, and all spiritual consolation was denied". Then, in the safe refuge of Rome, he raised his voice for the relief of the oppressed, in numerous writings in which he characterized the "Holy Office of Portugal as a tribunal which served only to deprive men of their fortunes, their honor and their lives, while unable to discriminate between guilt and innocence; it was known to be holy only in name, while its works were cruelty and injustice, unworthy of rational beings, although it was always proclaiming its superior piety".
In 1773 and 1774 Pombaline Reforms abolished autos-da-fé and ended the Limpeza de Sangue (blood cleansing) statutes and their discrimination against New Christians, the Jews that had converted to Christianity, and their descendants regardless of genealogical distance, in order to escape the Portuguese Inquisition.
The Portuguese inquisition was extinguished in 1821 by the "General Extraordinary and Constituent assembly of the Portuguese Nation" .
In December 2008, the Jewish Historical Society of England (JHSE) published the Lists of the Portuguese Inquisition in two volumes: Volume I Lisbon 1540–1778; Volume II Évora 1542–1763 and Goa 1650–1653. The original manuscripts, assembled in 1784 and entitled Collecção das Noticias, were once in the Library of the Dukes of Palmela and are now in the library of the Jewish Theological Seminary in New York. The texts are published in the original Portuguese, transcribed and indexed by Joy L. Oakley. They represent a unique picture of the whole range of the Inquisition's activities and a primary source for Jewish, Portuguese, and Brazilian historians and genealogists.
The archives of the Portuguese Inquisition are one of the best preserved judicial archives of early modern Europe (with notable exception of the Goa tribunal). Portuguese historian Fortunato de Almeida gives the following statistics of sentences pronounced in the public ceremonies autos da fe between 1536 and 1794:
These statistics, although extensive, are not wholly complete, particularly in the case of Goa. The original documentation of this tribunal is almost entirely lost. List of autos da fé in Goa presented by Almeida has been compiled by the officials of the Inquisition in 1774, but is certainly only partial and does not cover the whole period of its activity. Some minor gaps concern also the remaining tribunals, i.e., there is no usable data about some fifteen autos da fé celebrated in Portugal between 1580 and 1640, while the records of short-lived tribunals in Lamego and Porto (both active from 1541 until c. 1547) are yet to be studied.
^Menachery G (ed) (1982) The St. Thomas Christian Encyclopedia of India, BNK Press, vol. 1.
^Menachery G (ed) (1998) "The Indian Church History Classics", Vol. I, The Nazranies, Ollur, 1998. ISBN 81-87133-05-8.
^Mundadan, A. Mathias. (1984) History of Christianity in India, vol. 1, Bangalore, India: Church History Association of India.
^Podipara, Placid J. (1970) "The Thomas Christians". London: Darton, Longman & Tidd, 1970 (a readable and exhaustive study of the St. Thomas Christians).
^Leslie Brown, (1956) The Indian Christians of St. Thomas. An Account of the Ancient Syrian Church of Malabar, Cambridge: Cambridge University Press 1956, 1982 (repr.)
^Thomas Puthiakunnel, (1973) "Jewish colonies of India paved the way for St. Thomas", The Saint Thomas Christian Encyclopedia of India, ed. George Menachery, Vol. II, Trichur.
^Koder S. "History of the Jews of Kerala". The St. Thomas Christian Encyclopaedia of India, Ed. G. Menachery,1973.
^T.K Velu Pillai, (1940) "The Travancore State Manual"; 4 volumes; Trivandrum)
^ abClaudius Buchanan (1811). Christian Researches in Asia: With Notices of the Translation of the Scriptures into the Oriental Languages. 2nd ed. Boston: Armstron, Cornhill
^ abvan der Ploeg, J.P.L., O.P. The Christians of St. Thomas in South India and their Syriac Manuscripts. Rome and Bangalore: Center for Indian and Inter-Religious Studies and Dharmaram Publications, 1983.
^The Imperio in the Azores - The Five Senses in Rituals to the Holy Spirit, Author: Maria Santa Montez, Instituto de Sociologia e Etnologia das Religioes, Universidade Nova de Lisboa, Lisboa; page 171
^BREVE NOTÍCIA DAS FESTAS DO IMPERADOR E BODO DO DIVINO ESPÍRITO SANTO, Padre Alberto Pereira Rei, Introdução: Manuel Gandra
^Descrição: Colectânea das principais Censuras e Interditos visando os Impérios do Divino Espírito Santo, Autor: Manuel J. Gandra - Boletim Trimestal do Centro Ernesto Soares de Iconografia e Simbólica - Outono 2009 
^Inquisição E Tradição Esotérica: O Neoprofetismo e a Nova Gnose, Da Cosmovisão Rosacruz Aos Mitos Ocultos De Portugal, Acção E Reacção No Colonialismo E Ex-Colonialismo Do Império Português - X - Culto do Espírito Santo - Profetismo - V Império - Sebastianismo - XI - Brasil e Goa, António de Macedo, Hugin Editores, Lisboa, 2003 
^The Imperio in the Azores - The Five Senses in Rituals to the Holy Spirit, Maria Santa Montez
^Descrição: Colectânea das principais Censuras e Interditos visando os Impérios do Divino Espírito Santo, Manuel J. Gandra