Montoya entered the Society of Jesus on 1 November 1606. In the same year, he accompanied Father Diego Torres, the first provincial of Paraguay, to this mission.
In co-operation with Fathers Cataldino and Mazeta, he founded the Reductions of Guayra. He also brought a number of tribal groups into the Catholic Church, and is said to have personally baptized 100,000 Indians. As head of the missions from 1620 he had charge of the "Reductions" on the upper and middle course of the Paraná River, on the Uruguay River, and the Tape River, and added thirteen further "reductions" to the twenty-six already existing.
When the missions of Guayra were endangered by the incursions of Paulistas from Brazil in search of slaves, Father Mazeta and Montoya resolved to move the Christian Indians, about 15,000 in number, to the reductions in Paraguay, partly by water with the aid of seven hundred rafts and numberless canoes, and partly by land through the forest. The plan was successfully carried out in 1631. "This expedition", says von Ihering, "is one of the most extraordinary undertakings of this kind known in history" [Globus, LX (1891), 179].
In 1637 Montoya (on behalf of the governor, the Bishop of Paraguay, and the heads of the orders) laid a complaint before Philip IV of Spain as to the Portuguese policy of sending kidnapping expeditions into the neighboring regions. He obtained from the king important exemptions, privileges, and protective measures for the reductions of Paraguay. Soon after his return to America, Montoya died.
Ruiz de Montoya was a fine scholar of the Guaraní language of the Amerindians, and left standard works on it. These are:"Tesoro de la lingua guaraní" (Madrid, 1639), a quarto of 407 pages;
"Conquista espiritual hecha por los religiosos de la Compañía de Jesús en las provincias del Paraguay, Paraná, Uruguay y Tape" (Madrid, 1639). A new edition was made at Bilbao: Corazón de Jesús (1892);
"Arte y vocabulario de la lingua guaraní" (Madrid, 1640), a quarto of 234 pages;
"Catecismo de la lingua guaraní" (Madrid, 1640), a quarto of 336 pages;
"Silex del Divino Amor" (1640), unedited in Montoya's times, the first edition was made in 1991 by the Pontifical Catholic University of Lima.
Marion Mulhall calls Ruiz de Montoya's grammar and vocabulary "a lasting memorial of his industry and learning". German linguist Georg von der Gabelentz regarded them as the very best sources for the study of the Guaraní language, while Hervas declares that the clearness and comprehensive grasp of the rules to which Montoya traced back the complicated structure and pronunciation of Guaraní are most extraordinary. All three works were repeatedly republished and revised. In 1876 Julius Platzmann, the German scholar in Native American languages, issued at Leipzig an exact reprint of the first Madrid edition of this work "unique among the grammars and dictionaries of the American languages". A Latin version was edited by the German scholar Christoph Seybold at Stuttgart in 1890-91. A collected edition of all Montoya's works was published at Vienna under the supervision of the Vicomte de Porto Seguro in 1876.
Of much importance as one of the oldest authorities for the history of the Reductions of Paraguay is Montoya's work, Conquista espiritual hecha por los religiosos de la C. de J. en las provincias del Paraguay, Paraña, Uruguay y Tape (Madrid, 1639), in quarto; a new edition was issued at Bilbao in 1892. In addition to the works already mentioned Montoya wrote a number of ascetical treatises.
Letters and various literary remains of Ruiz de Montoya are to be found in the "Memorial histor. español", XVI (Madrid, 1862), 57 sqq.; in "Litterae annuae provinc. Paraguariae" (Antwerp, 1600), and in the "Memorial sobre limites de la Repúbl. Argentina con el Paraguay" (Buenos Aires, 1867), I, appendix; II, 216-252; cf. Backer-Sommervogel, "Bibl. de la C. de Jesus", VI, 1675 sqq.