Very little is known about who this guy actually was, all of it fragmentary accounts. We have three first-hand accounts of him, one written by the Portuguese and two by the Japanese, and two mentions of him in later histories of the Catholic Church in Japan. 
This story, transmitted orally among both the Incan nobility in Cuzco and the common folk all across the Empire, reached Spanish years briefly after the conquest, told to conquistador Sarmiento de Gamboa by Inca nobleman Urco Guaranga, who owned the fabled horseskin and jaw. 
Born Pedro Chamijo in Seville, southern Spain, he came from a peasant family. He was a Mudéjar, meaning his family was originally Muslim but they had converted to Christianity. He was educated by Jesuits in Cádiz and set sail for the Americas at the age of 18. 
Ever since Mexican independence, factions within the clergy and the government wished to reform the church in Mexico, at first by reinstating the Mozarabic Rite, then later by completely cutting themselves off from Rome. Benito Juarez, a Freemason, was a known supporter of that. 