On the return of Albuquerque from Goa to Cananor, he was much rejoiced at the prospect of such powerful succours, and communicated his intentions of immediately resuming his enterprise against Goa, but was overruled in the council by Sequeira, on which Albuquerque went to Cochin, and obtained a victory over the Malabars of Calicut, who endeavoured to obstruct the Portuguese from loading pepper. Having dispatched Sequeira with the homeward bound ships, and soon afterwards Lemos with four more, he determined to resume the enterprise upon Goa. As Diego Mendez, who had formerly been favourable to this design, and several other captains, now opposed it, because it interfered with their intentions of going to Malacca, as directed by the king, Albuquerque commanded them all under the severest penalties not to quit the coast without his orders. Though much dissatisfied, they were obliged to obey. Accordingly, having fitted out twenty-three ships at Cananor, in which he embarked with 1500 soldiers, he proceeded to Onor to join his ally Timoja, whom he found busied in the celebration of his marriage with the daughter of a queen; and being anxious to have the honour of the viceroys presence at the wedding he invited him to land, which proved very dangerous, as they were kept on shore for three days in consequence of a storm, and when Albuquerque returned to the ships a boat with thirty men was lost. On leaving Onor for Goa, Timoja sent three of his ships along with Albuquerque, and promised to join him at Goa with 6000 men.

Albuquerque anchored for the second time before the bar of Goa on the 22d of November 1510. Impressed with a strong recollection of the dangers he had escaped from on the former attempt, and anxious to sooth the discontent which he well knew subsisted among some of his principal officers on account of having been reluctantly compelled to engage in this expedition, he addressed them in a conciliatory harangue by which he won them over entirely to concur with him in bringing the hazardous enterprise in which he was engaged to a favourable issue. Having made the proper dispositions for the assault, the troops were landed at early dawn on the 25th of November, and attacked the enemy who defended the shore with such determined intrepidity that they were put to flight with great slaughter, and without the loss of a man on the side of the Portuguese. The enemy fled and endeavoured to get into the city by one of the gates, and being closely pursued by the Portuguese who endeavoured to enter along with them, the fight was there renewed, till at length many of the Portuguese forced their way into the city doing prodigious execution, and the battle was transferred to the streets. These were successively cleared of the enemy by dint of hard fighting all the way to the palace, in which time the Portuguese had lost five officers of some note, and the fight was here renewed with much valour on both sides. Albuquerque, who had exerted himself during the whole action with equal courage and conduct, now came up with the reserve, and the Moors were completely defeated, flying in all directions from the city and endeavouring to escape to the continent, but through haste and confusion many of them perished in the river. After this decisive victory, it was found that of 9000 men who defended the city, 6000 had perished, while the Portuguese lost fifty men. Medeorao121, or Melrao, nephew to the king of Onore, who commanded the three ships sent by Timoja, behaved with great courage and fidelity on this occasion; Timoja came himself to Goa with a reinforcement of 3000 men, but too late to assist in the attack, and was only a witness to the carnage which had taken place. The booty in horses, artillery, arms, provisions, and ships, was immense, and contributed materially to enable Albuquerque to accomplish the great designs he had in contemplation.

The Portuguese who were slain in this brilliant exploit were all honourably interred; those of the enemy were made food for the alligators who swarmed in the river. All the surviving Moors were expelled from the city, island, and dependencies of Goa, and all the farms were restored to the gentiles, over whom Timoja was appointed governor, and after him Medeorao, formerly mentioned. While employed in settling the affairs of his conquest, ambassadors came from several of the princes along the coast to congratulate Albuquerque on his brilliant success. Both then and afterwards, many of the officers of Adel Khan made inroads to the neighbourhood of Goa, but were always repelled with loss. At this time, Diego Mendez and other two captains belonging to his squadron, having been appointed by the king of Portugal for an expedition to Malacca, stole away from the port of Goa under night in direct contravention of the orders of Albuquerque, intending to proceed for Malacca. Albuquerque sent immediately after them and had them brought back prisoners; on which he deprived them of their commands, ordering them to be carried to Portugal to answer to the king for their conduct, and condemned the two pilots who had conducted their ships from the harbour to be immediately hung at the yard-arm. Some alleged that Albuquerque emulously detained Diego Mendez from going against Malacca, which enterprise he designed for himself, while others said that he prevented him from running into the same danger which had been already met with by Sequeira at that place, the force under Mendez being altogether inadequate to the enterprise.

To provide for the future safety of Goa, Albuquerque laid the foundations of a fort, which he named Manuel, after the reigning king of Portugal. On this occasion, he caused the names of all the captains who had been engaged in the capture of Goa to be engraven on a stone, which he meant to have put up as a monument to their honour; but as every one was desirous of being named before the others, he turned down the stone so as to hide all their names, leaving the following inscription,

Lapidem quem reprobaverant aedificantes.

Thus they were all pleased, rather wishing their own individual praises to be forgotten, than that others should partake. Albuquerque assuming all the powers of sovereignty in his new conquest for the king of Portugal, coined money of gold, silver, and copper, calling the first Manuels, the second Esperas, and the third half esperas. Resolving to establish a permanent colony at this place, he engaged several of the Portuguese to intermarry with the women of the country, giving them marriage portions in lands, houses, and offices as an encouragement. On one night that some of these marriages were celebrated, the brides became so mixed and confounded together, that some of the bridegrooms went to bed to those who belonged to others; and when the mistake was discovered next morning, each took back his own wife, all being equal in regard to the point of honour. This gave occasion to some of the gentlemen to throw ridicule on the measures pursued by Albuquerque; but he persisted with firmness in his plans, and succeeded in establishing Goa as the metropolis or centre of the Portuguese power in India.

The king of Portugal had earnestly recommended to Albuquerque the capture of the city of Aden on the coast of Arabia near the entrance of the Red Sea; and being now in possession of Goa, he thought his time mispent when not occupied in military expeditions, and resolved upon attempting the conquest of Malacca; but to cover his design, he pretended that he meant to go against Aden, and even sent off some ships in that direction the better to conceal his real intentions. Leaving Don Rodrigo de Castel Branco in the command of Goa with a garrison of 400 Portuguese troops, while the defence of the dependencies and the collection of the revenue was confided to Medeorao with 5000 native soldiers, Albuquerque went to Cochin to prepare for his expedition against Malacca.