In 1560, the Spanish rulers of Peru sentenced Lope de la Pena, described as a "Moor from Guadalajara", to life imprisonment for the crime of "having practiced and spread Islam" in Cuzco and was also required to wear the Sanbenito around his neck for his entire imprisonment. Other sources give his name as Alvaro Gonzalez.
His colleague, the mulatto "son of a Spaniard [Juan Solano] and a black woman", Luis Solano was similarly convicted of spreading Islam, but was executed for the offence.
As persecution increased in the Spanish dependencies, Muslims ceased identifying themselves by their religion and became nominal Christians; eventually Islam disappeared from the country entirely.
In 1911, the Peruvian missionary McNairn wrote about "God's call to His Church to go in and possess the land [in] Africa, in view of the great Moslem advance. We must take the Light to the Dark Continent before the apostles of Mohammedanism enshroud it in yet greater darkness".
Islam was reintroduced to Peru in the 1940s, during the Palestinian exodus, Palestinian and Lebanese Muslims fleeing from the Arab-Israeli war.
In 1974, the Nation of Islam, through its counterpart in Belize, began importing Pacific Whiting fish from Peru to the United States, where it was sold as an Islamic alternative to mainstream fish markets.
In 1993, the Muslim community opened a masjid in the Jesús María District of the capital, but it was later closed due to financial difficulty. Another location was opened in the Villa El Salvador district, but met with similar difficulties and also closed.