His collection was poetically described as early as 1613 by Scipione Francucci. In 1607, the Pope gave the Cardinal 107 paintings which had been confiscated from the studio of the painter Cavalier D'Arpino. In the following year, Raphael's Deposition was secretly removed from the Baglioni Chapel in the church of San Francesco in Perugia and transported to Rome to be given to Scipione through a papal motu proprio. The Borgheses were forced to provide Perugia with two excellent copies of the painting to avoid conflict with the angered city becoming violent, but the original remains in the Borghese collection.