- For similarly named individuals, please see Juan Borgia.
The order of the two elder brothers was reversed from the Showtime series, with Juan being the elder in the Canal+ series. Historians commonly believe that Juan was in fact Rodrigo's oldest surviving son.
Juan, like his brother Cesare was known for his sexual appetite. He carried on affairs with a number of women. In one case he was caught in the act by Virginio Orsini carrying on with his wife. Juan fled, leaving the poor woman to be murdered by Orsini. When his father found out he shrugged and stated that Orsini should be fined for the act.
After his father became Pope Alexander VI, Juan was named the 2nd Duke of Gandia and the Captain-General of the Church (leader of the Papal Armies).
Even though Juan was named to leadership posts he was rather incompetent. Brushing off the assistance of capable men, he led the Papal armies to devastating defeats. After a crushing defeat at the Orsini stronghold in Bracciano Virginio Orsini sent a donkey with a sign around its neck declaring it to be the Prefect of Rome. Orsini had also lodged a message for Juan in the donkey's rear end informing Juan that Orsini could shove whatever he wanted up Juan's rear end.
As Juan's blunders began to mount up tension increased between him and his family. Juan nearly raped his sister Lucrezia and fought with his brother Cesare. After a family gathering broke down into an argument between Juan and the rest of his family he rode off to party. It would be Lucrezia who finally had enough of her brother, and with the assistance of her lover Perotto murdered him.
A short time later Juan's body washed up in the Tiber river. The ducats he had been carrying were still on him. Juan's body was taken to the Vatican where it was properly cleaned, dressed, and funeral rites held. The death of his son devastated Alexander, who spent several days raging over the death of his son while his family and his mistress Giulia Farnese spent the time praying outside his chambers.
Just before Pope Alexander's own death a few years later he experienced a vision where Juan's eventual grandson (and Alexander's great-grandson) Saint Fracncis Borgia appeared to guide him into the afterlife. Alexander was pleased to learn that a member of the Borgia clan would ascend to the Sainthood, but was less than pleased when Francis pulled him away from his Earthly existence.
Juan had initially been buried in Rome, however his body was later removed at the orders of Julius II to the family chapel in Gandía. After escaping from King Ferdinand his brother Cesare visited his remains at the Borja chapel, and met Juan's son and daughter for the first time.