Marroquín was born near Santander, Spain. He studied philosophy and theology in Osuna. After entering the priesthood, Marroquín became a professor at the University of Osma where he met Bishop García de Loaisa, an adviser to Emperor Charles V. Marroquín became a priest in the Spanish royal court. In 1528 the conquistador Pedro de Alvarado, Governor of Guatemala, was in Spain and met Marroquín; he convinced the priest to accompany him back to Guatemala.
After first arriving in Mexico, he traveled onwards to Guatemala with Alvarado, in May 1528. On April 11, 1530, he was appointed parish priest of Guatemala. On December 18, 1534, he was made bishop of Santiago and later provisional governor of Guatemala.
Marroquín founded the School of Saint Thomas in 1559 (now the University of San Carlos of Guatemala) as part of his efforts to educate the native people. He became a scholar of the K'iche' language and published the first catechism in that language.
Although Universidad Francisco Marroquín is named after him, the university does not follow any of his philosophies or teachings.
- Recinos 1952, 1986, p. 127. n. 75.
- Recinos 1952, 1986, p. 127.
- Pérez de Antón, Francisco (January 13, 1992). "In Praise of Francisco Marroquín". Universidad Francisco Marroquín, Guatemala City.
- Recinos 1952, 1986, pp. 126-127.
- "Francisco Marroquín (1499 - 1563)" (pdf). Religion & Liberty (Grand Rapids, Michigan: Acton Institute for the Study of Religion and Liberty) 12 (5). September and October 2002. Retrieved 2008-10-14. [dead link]
- "Francisco Marroquin (1478-1563)" (Spanish). Genesis Megaprogramas, SA. Retrieved 2008-10-14.