Arriving in Rome following Valentino, Catherine was received by the pontiff in a cordial manner, and in an equally cordial manner she was proposed to sign a formal renunciation of the dominion of the lands of Romagna. Caterina flatly refused. «She is devilish and strong of spirit» – as the chronicles of the time wrote. She was thus locked up in the Belvedere palace and controlled by a guard of honor night and day. Despite this, towards the end of May she managed to try to escape. It failed and she was locked up in the papal prisons at Castel Sant’Angelo. In order to justify the countess’s imprisonment to the French, to whom the Borgias had assured that they would treat her as a guest and not as a prisoner, they invented the accusation against Catherine of having tried to kill the pontiff through poisoned letters, sent him from Forlì in November 1499.
She spent the last years of her life in the Medici villa, called Castello and in the other residences owned by the family of her husband Giovanni. She died in Florence on May 28, 1509, at the age of forty-six: she had velvet skin and blond hair.
Her body was buried in the monastery of the Murate in Florence, in front of the main altar. Her nephew Cosimo I de ‘Medici, Grand Duke of Tuscany, subsequently had placed a plaque on her tomb, however today no trace of the tomb of Catherine remains.