A post from 2012:
Did Cesare Borgia kill Juan Borgia?
In my e-mystery, A Borgia Daughter Dies, the first corpse is plucked from the Tiber by the same fisherman who found Juan's body, and became famous because. . . .well, enough of that. If you want to know, A Borgia Daughter Dies will tell you exactly what happened and when, in a fun way.
Cesare Borgia may well have killed his brother Juan, or had him killed, to escape from ecclesiastical orders and become the chief soldier of the papacy. But no one knows for sure. It's obvious that his own father suspected him, from the pope's behavior at the time. Ultimately, Cesare either persuaded his father that the accusation was false, or the pope decided to forgive his most competent son. Pope Alexander VI could forgive much, but it seems unlikely he could forgive fratricide, particularly since his love for Juan was made clear by the extremes of his mourning. So I vote for Cesare's powers of persuasion.
It is very unlikely that Lucrezia had anything to do with Juan's murder, contrary to the Showtime miniseries. Juan did not threaten baby Giovanni Borgia, who was born after Juan died. And Juan didn't kill Lucrezia's lover, who was not named Paolo and was not a stable boy. Cesare did. (See my earlier blog on this subject, if you want the details. Or read A Borgia Daughter Dies.)
But there were certainly other suspects. The Showtime series could have blamed Caterina Sforza, who had vowed vengeance for Juan's treatment of her son. These events were fictional, but in real life Juan had botched a siege of an Orsini castle, and the Orsini were angry because Virginio Orsini had died abruptly in the Castel Sant'Angelo, where the pope had imprisoned him for siding with the French army in the recent invasion. They were sure Virginio was poisoned, and he may well have been. Secret vengeance by killing a relative was part of the vendetta culture in Italy at the time, and the Orsini /Borgia vendetta dated back at least to the reign of the first Borgia pope, Calixtus III. And the nine stab wounds, all over Juan's body and legs, suggest multiple assailants who wanted vengeance. Cesare and Michelotto were killers, but they were rational and efficient ones. Something that messy doesn't seem like their style.
There were also rumors that a wronged husband, father or brother killed Juan, who was definitely pushy, arrogant and promiscuous. One thing is certain: it wasn't a robbery. Juan's body still bore a rich purse when it was pulled from the Tiber. And the fisherman who found it became famous because. . . . Oh, right. You can read the story in A Borgia Daughter Dies. I believe the first pages are free--you can easily find the answer there.