John de Austria completed his education at the University of Alcalá de Henares (now the Complutense University), where he attended with his two young nephews, who were about his same age: Prince Carlos (son and heir of Philip II) and Alessandro Farnese, Prince of Parma (son of Charles V's other acknowledged illegitimate child, Margaret of Austria, Duchess of Parma). They all had Honorato Hugo (disciple of Juan Luis Vives) as a teacher. In 1562, the "House of Don John of Austria" appears in the budget of the Royal House, assigning to him 15,000 ducats, the same amount allocated to his half-sister Joanna, Dowager Princess of Portugal, with whom John had a close relationship.