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.

In Lima, the community is based in the upper-class districts of San Isidro and Miraflores, where a number of synagogues are also located.

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.

Their mixed-race descendants, known today as the Amazonian Jews, were reared with syncretic Catholic, Jewish, European, and Andean rituals and beliefs.

[10] 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.

[7][9] According to anthropologist Irene Silverblatt, though it is not clear that those who were persecuted under the inquisition were practicing Judaism, most of the New Christians in Lima were considered "tainted" even after being baptised.

A notable figure of those prosecuted in Lima included Manuel Bautista Pérez, an individual who was considered as "one of the world’s most powerful men in international commerce".

[8] Some of the evidence submitted in the trial included many New Christians appearing as witnesses calling him the Great Captain of Jews in Peru, along with his brother-in-law denouncing him.

[13] Starting in 1885, the Amazon rubber boom attracted even greater numbers of Sephardi Jews from North Africa as well as Europeans.

After the boom fizzled due to competition from Southeast Asia, many European and North African Jews left Iquitos.

[6] A notable resident at the time was Auguste Dreyfus,[6] who had signed a contract with the Peruvian government to acquire 2 million tons of guano.

Around 1912, some Ashkenazi Jews, mostly from Western and Eastern Slavic areas and from Hungary, also made the same voyage, chiefly to the capital Lima.

[14] Meanwhile, the Ashkenazi Unión Israelita del Perú was founded at the Chirimoyo neighbourhood on June 11, 1923, which was officially registered on November 16, 1929.

[17] During this decade, the Unión Israelita del Perú—the Ashkenazi congregation of Peru established in 1923—hired Abraham Moshe Brener, a Polish Rabbi, to perform Jewish rituals in the country.

[17] During the 1930s, the community saw itself negatively affected with the establishment of the Revolutionary Union, a fascist political party founded by Luis Miguel Sánchez Cerro, who served as president from 1931 until his assassination in 1933.

[19] For logistical reasons, and in response to growing anti-Jewish sentiment, the Directorio de la Colectividad Israelita del Perú was established on February 4, 1942, presided by Max Heller, Jacobo Franco and Leopoldo Weil.

[14] Another "Pro-Hebrew Palestine" committee was established on June 27, 1945, headed by José Gálvez Barrenechea and composed of people such as Luis E. Valcárcel and César Miró, among others.

[22] The congregation eventually unified again,[17] starting with the dissolution and reincorporation of the members of Knesset Israel and Adat Israel, followed by a process of integration between Sharón and the Unión Israelita that started in 1987, when the inventory of the synagogue of the Unión Israelita located at Brasil Avenue was moved to the former's location in San Isidro.

[22] During World War II, the Consul-General of Peru in Geneva, José Maria Barreto, secretly issued passports to a group of Jews which included prisoners at the concentration camp in the (German-occupied) French city of Vittel.

The Peruvian government at the time had forbidden its diplomatic missions to issue visas to Jewish refugees,[23] an order that Barreto ignored.

[citation needed] During a trip to Iquitos in 1948 and 1949, the Argentine-Israeli geologist Alfredo Rosensweig had noted that the Amazonian Jews were "almost a hidden community" due to their geographical separation from Lima and the city's inaccessibility by road.

[13] The community of Iquitos Jews had not been recognised by the rest of Peru until the 1980s, when Rabbi Guillermo Bronstein, who was then the chief rabbi of the Asociación Judía del Perú in Lima, was contacted by the Iquitos Jews and visited the community in 1991, subsequently sending resources such as prayer books and other Jewish texts.

In the late 20th century, some descendants in Iquitos began to study Judaism and eventually made formal conversions in 2002 and 2004 with the aid of a sympathetic American rabbi from Brooklyn.

[4] The Fire Within: Jews in the Amazonian Rainforest (2008) is a documentary about the Jewish descendants in Iquitos and their efforts to revive Judaism and emigrate to Israel in the late 20th century.