João received a military education and was a colonel of a cavalry regiment. He was visiting England and France with his brother the Duke of Porto, heir presumptive to the throne, when they were summoned to return to Portugal by their brother King Pedro V who was dying of typhoid fever or cholera. Their brother died on 11 November 1861 before they could return along with their fifteen year old brother Fernando. With his death the Duke of Porto became King Luís I and João became heir presumptive to the throne.
He did not remain heir for long as he died a month later of the same illness that killed his brothers in Lisbon on 27 December 1861 aged 19 and unmarried.
The House of Saxe-Coburg and Braganza was not a recognized house in the former Kingdom of Portugal and monarchs following Maria II and Ferdinand II officially continued to be members of the House of Braganza