The infante died in summer 1468 and was replaced as pretender to the throne by his sister Isabella. Carrillo acted as her main advisor and with Pedro de Peralta (Pedro de Peralta y Ezpeleta) he played a major part in arranging her marriage to Ferdinand II of Aragon in October 1469. Even so, when the Catholic Monarchs came to power after Henry IV's death in December 1474, they immediately came into conflict with Carrillo. Carrillo would not accept their authoritarian treatment of him nor his enemy cardinal Pedro González de Mendoza's rise to be chancellor of the kingdom. This led him to clash with the Mendoza family, a battle he lost in the War of the Castilian Succession that followed (1475–1479). Completely changing his policy, Carrillo joined the camp led by the king of Portugal, which supported the claim to the Castilian throne by his niece, princess Joanna la Beltraneja, against the claim of Isabella I.