While Albuquerque rested and refreshed his men on board, Mahomet was busily employed in making every possible preparation for defending the city. For this purpose he undermined the streets in several places, in hopes to blow up the assailants, and strewed poisoned thorns in the way, covering them over to prevent their being observed. He likewise fortified the bridge, and planted cannon in many places. As a prelude to the second assault, Albuquerque sent Antonio de Abren in a vessel well manned to gain possession of the bridge. On his way thither he had to pass through showers of bullets from both sides of the river and from the battlements of the bridge, and though desperately wounded, refused to be brought off, when Deniz Fernandez Melo, who came up to his rescue proposed sending him to the ships to have his wounds dressed, saying, "Though he neither had strength to fight nor voice to command, he would not quit his post while life remained." Floats of wildfire were sent down the river to burn the vessel; but at length Albuquerque in person gained possession of the bridge, and the vessel being freed from the fire rafts, had liberty to act against the enemy. Having rested his men a short time on the bridge, Albuquerque penetrated the city, through showers of bullets, darts, and arrows; and having been apprised of the mines in the principal street, he took, another way and gained the mosque. At length, after a prodigious slaughter of the enemy, he gained entire possession of the city, having only with him in this action 800 Portuguese and 200 Malabars.

At the end of nine days every one of the Moors who inhabited this great city were either slain or driven out, and it was repeopled with strangers and some Malays, who were permitted to take possession of the vacant houses. Among these last was Utimuti rajah, whose son had formerly endeavoured to assassinate Sequeira. Utimuti was a rich and powerful native of Java, of whom more hereafter. The soldiers were allowed to plunder the city during three days. There were found 3000 pieces of great cannon, out of 8000127 which King Mahomet had relied upon for the defence of his city, the rest having been carried off to Bintang, where the king and prince Al'oddin had fortified themselves. As it might have been of dangerous consequence to permit these princes to establish themselves so near the city of Malacca, Albuquerque sent a force to dislodge them, consisting of 400 Portuguese, 400 Malays belonging to Utimuti, and 300 men belonging to the merchants of Pegu who resided in Malacca. On the approach of these troops, the king and prince took flight, leaving seven elephants with all their costly trappings, and the Portuguese returned to Malacca. Now reduced to wander in the woods and mountains of the interior, Mahomet so severely reflected upon the obstinacy of his son and the king of Pahang, that he and his son quarrelled and separated, each shifting for himself.

To secure this important conquest, Albuquerque built a fort or citadel at Malacca, which from its beauty was called Hermosa. He likewise built a church, which was dedicated to the Visitation of our Lady; and coined money of different values and denominations, which was ordered to pass current by proclamation, and some of which he caused to be scattered among the populace. By these and other prudent measures he gained the hearts of the people, attracted strangers to settle in Malacca, and secured this important emporium of trade. Although Albuquerque was perfectly conscious of the deceitful character of Utimuti rajah, yet considering it to be sometimes prudent to trust an enemy under proper precautions, he gave him authority over all the Moors that remained in Malacca. It was soon discovered however, that Utimuti carried on a private correspondence with Prince Al'oddin, under pretence of restoring him to the sovereignty of Malacca, but in reality for the purpose of using his remaining influence among the people to set himself up. On receiving authentic information of these underhand practices, Albuquerque caused Utimuti with his son and son-in-law to be apprehended, and on conviction of their treason, he ordered them to be publicly executed on the same scaffold which they had formerly destined for Sequeira. This was the first public exertion of sovereign justice which was attempted by the Portuguese in India, but was soon followed by others. Pate Quitir, another native of Java, whom Albuquerque appointed to succeed Utimuti in the government of the Moors in Malacca, was gained by the widow of Utimuti, by promise of her daughter in marriage with a portion of 100,000 ducats, to revenge the death of her husband on the Portuguese, and to assassinate Albuquerque. Quitir accepted her offer, meaning to seize the city for himself. About the same time also, the king of Campar formed a similar design, for the attainment of which purpose he sent a congratulatory embassy to Albuquerque, from whom he demanded the office which had been conferred on Quitir. These plots having no consequences at this time, shall be farther explained in the sequel.

During his residence at Malacca, Albuquerque received embassies from several princes, particularly from the king of Siam; and he sent likewise embassies in return, to the kings of Siam and Pegu. He sent also two ships to discover the Molucca islands and Banda128, and gave orders to let it be known in all quarters that Malacca was now under the dominion of Portugal, and that merchants from every part of India would be received there on more favourable terms than formerly. Having now established every thing in Malacca to his mind, Albuquerque determined upon returning to Cochin, leaving Ruy de Brito Patalim to command the fort with a garrison of 300 men. He left at the same time Fernando Perez de Andrada with ten ships and 300 soldiers to protect the trade, and carried four ships with himself on his return to Cochin.

During these transactions at Malacca a rebellion broke out among the natives at Goa, taking advantage of which, Pulate Khan, an officer in the service of Kufo Adel Khan king of Bisnagar passed over into the island of Goa with considerable army, and laid siege to the city. One of the principal exploits during this siege was a sally made by Rodrigo Robello de Castello Franco the governor, in which the besiegers suffered considerable loss. But Rodrigo was soon afterwards slain, and Diego Mendez de Vasconcellos was chosen to take the command by the universal suffrages of the besieged. At this time Adel Khan became jealous that his general Pulate Khan intended to usurp the sovereignty over the territory of Goa, on which account he sent his brother-in-law, Rotzomo Khan to supersede him, who entered into a treaty with Diego Mendez, by whose assistance he got the mastery over Pulate Khan. Finding himself at the head of 7000 men, while there were not above 1200 troops in the city of Goa, 400 only of whom were Portuguese, Rotzomo resolved to endeavour to drive them out, and resumed the siege. Being short of provisions, the besieged began to suffer severely from famine, and several of the men deserted to the enemy, some of whom repented and returned to the city. In this critical situation, Emanuel de la Cerda who had wintered at Cochin fortunately arrived with succours, and was followed soon after by Diego Fernandez de Beja, who had been sent to demolish the fort at Socotora, and to receive the tribute at Onnuz. By these the besieged were abundantly relieved and succoured with recruits and provisions when almost reduced to extremity. Soon afterwards arrived Juan Serram who had gone from Portugal the year before with Peyo de Sa, in order to settle a trade in the island of Madagascar, but ineffectually; and Christopher de Brito, who happened to be at Cananor with a large ship and four smaller vessels, where he heard of the distressed situation of Goa, went immediately thither with a strong reinforcement and an ample supply of provisions.