Malacca, defended by some twenty thousand mercenaries and two thousand artillery pieces, was a focal point in the regional trade network attracting merchants from Gujarat, China, Japan, Java, Bengal, Persia and Arabia but despite its wealth, Sultan Mahmud Shah's government was unpopular with non-Muslim traders. The fall of the city after two attacks spaced seventeen days apart was at least partly due to assistance received from foreign merchants in the port.
Having made a bold approach to the city, demanding the release of the nineteen prisoners, the payment of damages and consent to build a fortified trading post. Albuquerque got the prisoners back, but the Sultan, unconvinced by the size of the Portuguese force was unwilling to deliver any further concessions.
An attack at dawn on 25 July established a Portuguese foothold in the city, and merchants seeking Portuguese protection received banners to mark their premises, which would not be ransacked. The second attack on 15 August delivered control of the city, which was selectively looted.
Albuquerque then set about strengthening Malacca's defences against an anticipated Malay counterattack, and the Portuguese fortress, constructed from stones taken from the mosque and the cemetery, was complete by November 1511.
Now that Malacca was under Portuguese control, Albuquerque sailed for India on 20 November aboard the Flor de la Mar, the largest carrack built for service in the Indies. He needed the ship's capacity to hold the treasure looted in the conquest of the city, a gift from the King of Siam and his personal fortune, but the vessel was unsound.
The Flor De La Mar went down in a storm off Sumatra, Albuquerque barely escaped with his life and, in the meantime events, in Goa had seen the city change hands.
Forces loyal to the Sultan of Bijapur, the former ruler had taken over thanks to Albuquerque's Portuguese rivals, who had opposed the conquest and were convinced that it would be best to let it go.