Albuquerque abandoned the city in August but was back on 25 November with a reinforced fleet. Diogo Mendes de Vasconcelos had been en route to take Malacca before he was persuaded to change his priorities. His ships and men, along with Albuquerque's forces and about three hundred local troops from Cannanore were enough to overpower Goa's nine thousand defendants. Six thousand of them are reputed to have died, killed in the battle or drowned while attempting to escape.
Seizing Goa delivered a permanent Portuguese base in the Indies, though it came under constant attack and changed hands while Albuquerque attended to matters further east, where the nineteen Portuguese captives who had participated in Diogo Lopes de Sequeira's failed embassy in 1509 were still incarcerated.
A letter from one of the nineteen, Rui de Araújo, reached Albuquerque in February 1511, through the hands of a Hindu merchant gave details of Malacca's defences. Albuquerque used the letter as a justification to attack the city with a combined fleet. With Goa's defences strengthened, he set off for Malacca in April 1511 with about eighteen ships, nine hundred Portuguese and two hundred Hindu mercenaries despite the protests of Diogo Mendes de Vasconcelos, who claimed the expedition was rightfully his to command.
Ferdinand Magellan, who had been part of de Sequeira's embassy in 1509, was one of the Portuguese participants in the expedition.