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- For his similarly named relatives, see Juan de Borja.
Pope Sixtus IV, also a relative, made Borja protonotary apostolic and an editor of apostolic letters circa 1408. Pope Innocent VIII made him the Governor of Rome. Borja had an illegitimate son named Galcerán.
After the papal conclave, 1492, which elected Borja's relative Rodrigo pope as Alexander VI, he was created cardinal-priest of S. Susanna on August 31, 1492. He was later elected archbishop of Monreale on September 13, 1483, an archdiocese he would never visit but occupy until his death. There is no evidence he was ever ordained a priest or consecrated as bishop.
Borja went on to accumulate benefices and their associated revenues: he became the administrator of the see of Olomouc, Moravia from February 8, 1493 to January 30, 1497. He was named legate a latere to Alfonso II of Naples on April 18, 1494.Borja was named bishop of Ferrara on October 29, 1494, taking possession of the see on June 14, 1497 until his death. He was also the bishop of Melfi from September 19, 1494 until death, occupying it from December 3, 1498.
In May 1494, he attended the coronation of Alfonso II of Naples (whose son, Alfonso of Aragon, is widely believed to have been later strangled by Borja's cousin Cesare after marrying Lucrezia Borgia), along with one patriarch, seven archbishops, and forty bishops; Borja himself crowned Alfronso king on May 18. Along with Cesare Borgia and Alexander VI, Juan met with Alfonso on July 12, 1494 in Vicovaro to co-ordinate military strategy against Cardinal Ascanio Sforza (whom Borja would later replace in the lucrative office of the Vice-Chancellor in 1500) and his allies as well as Charles VIII of France. He brought Alexander VI's terms of peace to Charles VIII on December 25, 1494 in Bracciano before retreating with the pontiff on January 7, 1495 to the Castel Sant'Angelo (and then on May 27, 1495 to Orvieto) to take refuge from French troops. On April 24, 1503, Borja became the titular Latin Patriarch of Constantinople.
- Chambers, D.S. 2006. Popes, Cardinals & War: The Military Church in Renaissance and Early Modern Europe. I.B. Taurus. ISBN 1-84511-178-8.