The history of the Jews in Peru dates back to the country's Spanish period with the arrival of migration flows of Sephardic Jews from Europe, the Near East and Northern Africa. This small community virtually disappeared as a result of the Inquisition, and was only revived by two migratory waves that took place during the late 19th-century and the early to mid-20th century, with a number of Sephardic and Ashkenazi Jews arriving to northeastern Iquitos due to the Amazon rubber boom, as well as the country's capital, Lima, through neighbouring Callao, where they also settled due to World War II.

The small community in and around Iquitos is now known as the Amazonian Jews, most of which have since established themselves in Israel since the late 20th century. In Lima, the community is based in the upper-class districts of San Isidro and Miraflores, where a number of synagogues are also located. A synagogue also services a small community in the southern city of Cuzco.

Some Jewish conversos arrived at the time of the Spanish conquest of the Inca Empire. Then, only Christians were allowed to take part in expeditions to the New World. At first, they had lived without restrictions because the Inquisition was not active in Peru at the beginning of the Viceroyalty. According to the Jewish Virtual Library, the original attraction for Jews to come to Peru was the mineral potential. Many Jews had come to Portugal disregarding the immigration restrictions placed at the time. This action would then be used in trials against some of these crypto-Jews who faced the tribunal of Lima, further adding on a penalty to their actions.

The Holy Office of the Inquisition established an office in Lima January 9, 1570, to control the Christian population of the Viceroyalty and to identify non-Catholics, such as Jews, Lutherans, and Muslims. Consequently, 'New Christians' began to be persecuted, and, in some cases, executed. Descendants of Jews were sometimes called "marranos" ("pigs"), converts ("conversos"), and "Cristianos nuevos" (New Christians) even if they had been reared as Catholics from birth. Crypto-Jews, self-proclaimed Catholics who would secretly adhere to Judaism, were the initial targets of the tribunal and punished, tortured or killed if caught. Some avoided the tribunals by immigrating out of Spanish territories, such as Peru.

To escape persecution, the conversos settled mainly in the northern highlands and northern high jungle. They intermarried with natives and non-Jewish Europeans (mainly Spanish and Portuguese people) in some areas, assimilating to the local people: in Cajamarca, the northern highlands of Piura (Ayabaca and Huancabamba), among others, due to cultural and ethnic contact with people of the southern highlands of Ecuador. Their mixed-race descendants, known today as the Amazonian Jews, were reared with syncretic Catholic, Jewish, European, and Andean rituals and beliefs.

According to historian Ana Schaposchnik, the stages of the trial followed "a sequence of: denunciation, deposition, imprisonment, hearings, accusation, torture, confession, defense, publication, sentence, and the Auto." The Auto de Fe were occasional public ceremony of punishments made through the inquisition. The punishments included being burnt to a stake, whipping, and being exiled. The trial had started with the accused being convicted of a crime.

The tribunal had often used their connections of viceroyalty to gain information about the New Christians, about their past actions in other Spanish colonies. This was the case of Joan Vincente, who was a Portuguese New Christian who had previously been renounced but was put into trial in 1603. His previous actions in Brazil, Potosi, and Tucumán had all been shared by the viceroyalties in those regions. The genealogies of the crypto-Jews were accessible through this connection, making it possible to accurately see who were New Christians. Since the actions of the accused was often not documented, the accused New Christians in court could not prove their statements, while the viceroyalty could obtain all the documentation needed in the trial.

In most trials, the accused New Christians would not give up names of others who were also known to be Judaizing, until they were tortured. After days or weeks of torture, most crypto-Jews gave up other crypto-Jews up to the tribunal. For example, Mencia de Luna, had said during the trial, "tell notaries of the tribunal to write whatever they wanted in her declaration, so that her suffering would come to an end". Schaposchnik also states that from recorded accounts from 1635 to 1639 of new Christian Portuguese, 110 people were arrested due to their alleged connection to the Great Jewish Conspiracy, with many having to reconcile their faith to Christianity along with being exiled and facing confiscation of property. He states, "As a result of the Auto General de Fe, the community of Portuguese New Christians in Lima were decimated." It is said that up 11 people were burned at a stake as they did not confess to committing any Judaic practices.