With his military resources stretched, Albuquerque was forced to sit out the monsoon in Cochin, waiting for reinforcements, which arrived on fleets commanded by Dom Garcia de Noronha (Albuquerque's nephew), and Jorge de Mello Pereira.
He sailed for Goa on 10 September 1512 with fourteen ships and seventeen hundred troops and laid siege to the city. Having breached the city's outer wall, Albuquerque's forces were about to launch the final assault when the defenders surrendered.
Some of Albuquerque's factional rivals had joined the local opposition, and while Albuquerque insisted that the renegades be handed over, he had to promise to spare their lives.
He did, but had them tortured and mutilated.
That seems to have been the end of dissent in the Portuguese ranks as Albuquerque set about imposing a centralised structure on Portuguese interests in the East. Previous notions about dividing the area into different spheres of interest went by the board.
When the Portuguese destroyed a Javanese fleet of three hundred ships and slaughtered eight thousand men off Muar in 1513, their hold on Malacca was secure.
But it was not all brute force. After Muslim and Gujarati merchants fled Goa and Malacca, Albuquerque set about persuading Southeast Asian and Chinese traders to work with the Portuguese. Diplomatic missions to Burma and Sumatra saw local rulers accept the new status quo, and a further mission to the Kingdom of Siam established amicable relations between Portugal and the most significant regional threat to Portuguese interests in Malacca.