Born in Cervera, he was an illegitimate son of Ferdinand II of Aragon by a Catalan noblewoman called Aldonza Ruiz de Ivorra (1454–1513).

His ecclesiastical career was determined by his father when he was five years old; his half-uncle, Juan de Aragón, Archbishop of Zaragoza and illegitimate son of King John II of Aragon, died.

Ferdinand II decided that Alonso would succeed him, but Pope Sixtus IV thought that he was too young and appointed Ausías de Puggio.

His father made him Lieutenant General of the Kingdom of Naples in 1507, to replace Gonzalo Fernández de Córdoba.

When Joanna's son and co-ruler, Charles I, arrived in November 1518, the Archbishop was confirmed as Lieutenant General of Aragon.