When the Cardinal-King died, the Duke accompanied the governors of the Kingdom to Lisbon and Setúbal, trying to assure recognition for his wife's claim, but ultimately gave up and accepted the rule of Philip II (future Philip I of Portugal). After the civil war that followed, Anthony, Prior of Crato was defeated at the Battle of Alcântara, and Philip II entered Portugal and was confirmed by the Cortes of Tomar, where João occupied the post of Constable.
