In 1563 he married his 1st cousin Infanta Catherine, daughter of Prince Edward, Duke of Guimarães and Isabel of Braganza (João's aunt).

Philip II of Spain (another grandson of Manuel I and also claimant to the throne), tried to bribe him to abandon his wife's pretensions, offering him the Vice-Kingdom of Brazil, the post of Grand-Master of the Order of Christ, a license to send a personal ship to India every year, and the marriage of his eldest son Teodósio of Braganza to one of his daughters (either Isabella Clara Eugenia or Catherine Michaela).

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.

When King Philip left to Spain, he endowed the post of Constable of Kingdom to João's heir Teodósio, 7th Duke of Braganza, a marquessate (Flexilla-Xarandilla) to his second son, Dom Duarte, and a commandment and many concessions to the third, Dom Alexandre, who was destined to become an ecclesiastic.

Through his marriage with Infanta Catherine of Guimarães were born: Media related to John, 6th Duke of Braganza at Wikimedia Commons