The Portuguese Inquisition, officially known as the General Council of the Holy Office of the Inquisition in Portugal, was formally established in Portugal in 1536 at the request of its king, John III. Although Manuel I had asked for the installation of the Inquisition in 1515 to fulfill the commitment of his marriage with Maria of Aragon, it was only after his death that Pope Paul III acquiesced. In the period after the Medieval Inquisition, it was one of three different manifestations of the wider Christian Inquisition, along with the Spanish Inquisition and Roman Inquisition. The Goa Inquisition was an extension of the Portuguese Inquisition in colonial-era Portuguese India.

The Inquisition was a judicial procedure and a group of institutions within the Catholic Church whose aim was to combat heresy, apostasy, blasphemy, witchcraft, and customs considered deviant. Violence, torture, or the simple threat of its application, were used by the Inquisition to extract confessions and denunciations from heretics. Studies of the records have found that the overwhelming majority of sentences consisted of penances, but convictions of unrepentant heresy were handed over to the secular courts, which generally resulted in execution or life imprisonment. The Inquisition had its start in the 12th-century Kingdom of France, with the aim of combating religious deviation, particularly among the Cathars and the Waldensians. The inquisitorial courts from this time until the mid-15th century are together known as the Medieval Inquisition. Other groups investigated during the Medieval Inquisition, which primarily took place in France and Italy, include the Spiritual Franciscans, the Hussites, and the Beguines. Beginning in the 1250s, inquisitors were generally chosen from members of the Dominican Order, replacing the earlier practice of using local clergy as judges.