Nothing is known of Dias’s subsequent private meeting with João II, though he certainly seems to have fallen from favour. He spent some time in in West Africa before João’s successor, Manuel I recalled him to serve as a shipbuilding consultant for Vasco da Gama's (c. 1460-1524).
Dias helped supervise the construction of the São Gabriel and the São Raphael and sailed with the expedition as far as the Cape Verde Islands, before returning to Guinea.
Two years later he was one of the captains of the thirteen-ship fleet Manuel assembled for the second Indian expedition, commanded by Pedro Álvares Cabral.
After making the first official discovery of the coast of Brazil on 22 April 1500, the fleet continued eastwards, encountering a massive storm on 29 May at what Dias had presciently named Cabo das Tormentas. Four of the thirteen ships, including Dias' command, went down with all hands.
Dias was survived by a son and daughter. His grandson Paulo Dias de Novais went on to govern Angola and founded the city of São Paulo de Luanda in 1576.