He wished to remarry, and a possibility which was canvassed was a match with Isabella of Scotland (1426–1494), the widow of Francis I, Duke of Brittany, after he died on 18 July 1450, but this was opposed by Charles VII of France.

Charles left three illegitimate children by three different mistresses: The ill feeling between father and son was increased when his father John took in 1447 for his second wife Juana Enriquez, a Castilian noblewoman (of a bastard cadet line from Castilian kings), who soon bore him a son, afterwards Ferdinand II of Aragon, and who regarded her stepson as an interloper.

When Joanna began to interfere in the internal affairs of Navarre, a civil war broke out, and in 1452 Charles, although aided by King John II of Castile, was defeated and taken prisoner.

In 1458 Alfonso died and John became king of Aragon, while Charles was offered the crowns of Naples and Sicily.

Aspiring to marry Isabella of Castile, he was then thrown into prison by his father, and the Catalans rose in his favor.