The great-grandson of both Pope Alexander VI and King Ferdinand II of Aragon, he was Duke of Gandía and a grandee of Spain.

His mother was Juana, daughter of Alonso de Aragón, Archbishop of Zaragoza, who, in turn, was the illegitimate son of King Ferdinand II of Aragon.

[2] His brother, Tomás de Borja y Castro, also entered the Church, becoming Bishop of Málaga, and later Archbishop of Zaragoza.

In Madrid in the month of September 1529, he married a Portuguese noblewoman, Leonor de Castro Mello y Meneses.

[citation needed] Upon Borgia's marriage, Charles V appointed him Marquess of Lombay, master of the hounds, and equerry to the empress.

[3] His diplomatic abilities came into question after his failed attempt at arranging a marriage between Prince Philip of Spain and the Princess of Portugal, thus ending a hope of bringing these two countries together, and resulting in his retirement as duke, handing his title to his son, Carlos.

[10] After that church was destroyed by arson in 1931, some of Borgia's ashes were recovered and eventually reinterred in the new Jesuit complex on calle de Serrano.

[18] Marc-Antoine Charpentier composed Motet pour St François de Borgia (H.354, for 1 voice, 2 treble instruments, and continuo) in his honor in the late 1680s.