João II. war mit seiner Cousine Eleonore von Viseu und Beja, einer Tochter seines Onkels Fernando, des Herzogs von Viseu und Beja, verheiratet.
"The Duke of Braganza [Ferdinand II. oder Fernando II.] took the lead in opposing the king’s decrees passed in the Cortes of Evora … For all these reasons John II. decided to strike a sudden and decisive blow, which should at once re-establish the power of the Crown and paralyze the feudal nobility with terror, and he therefore had the Duke of Braganza arrested, and executed, after a very short trial, at Evora, on June 22, 1483. The nobles, however, were not yet defeated, and they continued to intrigue against the king’s authority under the leadership of a yet nearer relation of his own, Diogo, Duke of Viseu and Beja [seinem Cousin und gleichzeitig Schwager], the eldest son of Dom Ferdinand ... But John II. was not dismayed … he determined not to spare his own relations, and on August 23, 1484, he stabbed the Duke of Viseu with his own hand in his palace of Setubal. This murder he followed up with decision: he had the Bishop of Evora, one of his father’s favourites, thrown down a well; and he executed, with or without trial, about eighty of the leading noblemen of the country. By these means John II. broke the power of the feudal nobility for ever … the fall of the nobility was followed by the absolutism of the monarch ... while at home he won the love of his people by reorganizing the government of the kingdom, and proved so good an administrator that the Portuguese gave him the title of 'the Perfect King.' It has been said that in his foreign policy John II. followed in the course set before him by John the Great. With the great monarchs then ruling in Spain, Ferdinand of Aragon and Isabella of Castile, he consistently remained on friendly terms, and in 1490 his only legitimate son, Affonso [1475-1491], was married to Isabella [(1470-1498)], eldest daughter of these sovereigns. The death of this son in the following year, without leaving children, was a terrible blow to him, but he nevertheless maintained his friendship with Ferdinand and Isabella, and in 1494 concluded the Treaty of Tordesillas with them. By this treaty, which was confirmed by a Bull, issued by Pope Alexander VI., the limits of the future possessions of the Spaniards and Portuguese in the regions explored and discovered by their mariners was fixed at 360º east of Cape Verde, and it was agreed that the Spaniards were to have full right to all lands discovered to the west of this line, and the Portuguese to all to the south and east." (in: H. Morse Stephens: The Story of Portugal, id., pp. 161-163).
João II. (oder Johann II.) führte die Projekte seines Großonkels Heinrichs des Seefahrers fort. Auch er wollte die Seeroute von Portugal nach Indien finden. Nichts anderes interessierte ihn. Daher beging er einen fatalen Fehler: "... he made the great mistake in 1493 of dismissing Christopher Columbus from his court as a visionary. He listened to all the arguments of the great discoverer with patience, but he did not agree with his conclusions that it was possible to reach India by sailing westwards across the Atlantic, and he therefore lost the opportunity of immortalizing his name and reign by a greater discovery than that of Vasco da Gama, the discovery of the vast continent of America. ... He greatly improved the art of ship-building, and encouraged the immigration of skilled shipwrights from England and Denmark; he did much to promote the improvement of fire-arms, and established a cannon foundry and a corps of artillery … and, above all, he patronized literature." (in: H. Morse Stephens: The Story of Portugal, id., p. 169).
Nach dem Tod seines einzigen legitimen Sohnes Alfonso war sein Cousin und Schwager Manuel I. (1469-1521), der jüngste Bruder seiner Gattin, sein Nachfolger auf dem portugiesischen Königsthron. "... a man in whom he could see no fit qualities for carrying on his own great schemes and projects. To oust him John II. thought of legitimatizing his illegitimate son by Anna de Mendonça, Dom Jorge, or George [1481-1550], whom he had made Grand Master of the Orders of Santiago and Aviz, but the reflection that on his death the country he loved so well would then be torn by civil war restrained him, and he did not interfere with the law of succession." (in: H. Morse Stephens: The Story of Portugal, id., p. 170). So wurde, als er am 25. Oktober 1495 starb, sein Cousin und Schwager Manuel I. der nächste König von Portugal