[2] After the election of Rodrigo Borja as Alexander VI, Francisco went to Rome, becoming a protonotary apostolic, and then the treasurer general on 20 September 1493.
He later accumulated a variety of additional benefices: first as Abbot commendatario of the monasteries of San Vincenzo al Volturno and of S. Stefano di Sermo, then the diocese of Terracina on 19 August 1495 and then the metropolitan see of Cosenza on 6 November 1499.
[4] He was made papal legate to Campagna in 1501, and left Rome on 22 June to retake Rocca di Papa and other estates of the Colonna for the papacy.
[4] From January 1503 to 1504, Borja held the title of Camerlengo, and during that time, on March 10, he attempted to recover some debts owed to the College of Cardinals.
Before death, Borja was briefly protoprete from January 1511, dying on 4 November 1511 in Reggio Emilia (where he is buried) before having had the opportunity to learn of his excommunication.