Having sailed from Onor accompanied by Timoja, Albuquerque came to anchor off the bar of Goa on the 25th of February 1510. As it was necessary to sail up the northern arm of the bay or river, on the bank of which the city was situated, Albuquerque sent his nephew Antonio de Noronha, accompanied by Timoja, to sound the channel. A light vessel of easy draught of water which led the way gave chase to a brigantine belonging to the Moors, which took shelter under protection of a fort or blockhouse, erected for protecting the entrance of the harbour, which was well provided with artillery and garrisoned by 400 men, commanded by Yazu Gorji, a valiant Turk. Seeing the other vessel in chase, Noronha pressed after him; and though the fort seemed strong, they attacked and took it after a stout resistance, during which the commandant lost greater part of one of his hands, yet persisted to defend his post till deserted by his men, when he too retired into the city. In the mean time, in emulation of his new allies, Timoja attacked and took another blockhouse on the continental shore of the channel leading to Goa, which was defended by some artillery and forty men. After these exploits the channel was sounded without any farther obstruction.

Next day, as Albuquerque was sailing up the channel to proceed in his enterprise, he was met by Mir Ali and other chief men of the city, who came to surrender it to him, only stipulating, that their lives, liberties, and goods should be secured. The reason of this surrender was because Gorji had terrified them by his account of the astonishing and irresistible prowess of the Portuguese, and because a Joghi, or native religious saint, had predicted a short time before, that Goa was soon to be subjected by strangers. Albuquerque readily accepted the surrender on the terms proposed, and having anchored before the town on the 27th of February, was received on shore by the inhabitants with as much honour and respect, as if he had been their native prince. Mounting on a superbly caparisoned horse which was brought for his use, he received the keys of the city gates, and rode in great pomp to the palace which had been built by Sabayo, where he found a great quantity of cannon, arms, warlike ammunition, and horses. Having issued orders and regulations which were much to the satisfaction of the inhabitants, he dispatched several messages or embassies to the neighbouring sovereigns, the only effect, of which was to shew his high spirit. Such of the neighbouring towns as were dependent upon God, sent deputations without delay to proffer their obedience and submission. The command of the fort or castle was given to Don Antonio de Noronha, the government of the infidels to Timoja, and the other offices were disposed of to the general satisfaction. Understanding that several ships belonging to Ormuz and other places on the Arabian coast, were lading in the port of Baticala, four Portuguese vessels were sent thither, which took and carried them to Cochin, and sent an ample supply of provisions to Goa.

About four months after the easy conquest of Goa, the fortune of Albuquerque began to change its appearance, as those persons in Goa on whose fidelity he had reposed most confidence, in spite of the remonstrances of Timoja, entered into plots to deliver up the place to its former master Ismael. They had submitted so easily to Albuquerque, because unprovided for effectual resistance, to save their properties, and to gain time till Ismael Adel Khan was prepared to come to their relief. Having at length completed his preparations, he sent on before him in June 1510 his general-in-chief Kamul Khan with 1500 horse and 8000 foot, on which Albuquerque took proper measures to defend his recent acquisition. Having detected a conspiracy of the Moors to deliver up the city, his first step was to secure and punish the chief conspirators; among these were Mir Cassem and his nephew, to whom he had confided the command of four hundred Moors, whom he caused to be hewed in pieces by his guards; several others were hanged in the most public places of the city, and the rest were rigorously imprisoned, above 100 being convicted of participating in the plot. By these rigid measures the city was terrified into submission.

Soon afterwards Kamul Khan approached with the van of the army of Ismael, and attempted to pass over into the island by means of boats which he had provided for that purpose. He was courageously opposed by Noronha, who captured twelve of the boats; many of the enemy were killed by the Portuguese, and many others devoured by the alligators which swarmed in the channel round the island; but at length Kamul Khan effected a landing in force on the island, and the Portuguese were obliged to take refuge within the walls of the city. Kamul Khan then invested the city with his army, which he began to batter with his cannon, and Albuquerque used every possible effort to defend the place. Ismael Adel Khan now came up to second his general, at the head of 60,000 men, 5000 of whom were cavalry. Part of this great army passed over into the island to strengthen the besiegers, and the rest took post in two divisions on the continent to prevent the introduction of provisions, one of these being commanded by an officer of reputation, and the other by the mother and women belonging to Ismael, who maintained their troops by the gain from 4000 prostitutes, who followed the camp. By the arrival of this vast army the city of Goa was completely surrounded, and no opportunity was left for Albuquerque to execute any enterprise against the numerous assailants. Making what was necessary prudent, he and his officers resolved to abandon the city before day, which was accordingly executed though with much hazard, the way being occupied by the troops of the enemy, and Albuquerque had his horse killed under him; yet he got off all his men without loss after a siege of twenty days.

After this retreat, it was resolved to spend the winter in these seas, for which purpose the fleet came to anchor in a bay, which although not commodious was the best that could be had on this part of the coast; and being incommoded by a fort named Pangi which had a considerable number of cannon, it became necessary to gain possession119. Accordingly 300 Portuguese troops were appointed for the assault, while Noronha had the command of a body of reserve, and Albuquerque guarded the shore. While the Portuguese prepared during the night to assail the fort next morning, 500 men marched by order of Ismael to reinforce the garrison; and when the Portuguese marched to the assault, both the Moorish garrison and the relief, being all drunk, mistook the Portuguese for friends; the garrison believing them to be the reinforcement, and the relief conceiving them to have been the garrison coming out to meet them. They were soon however fatally undeceived by the attack of the Portuguese, in which 340 of them were slain, and the rest put to the rout, while the Portuguese only lost one man who was drowned accidentally. A similar circumstance happened at the bulwark which had been formerly won by Timoja at Bardes. By these two severe defeats of his people, Ismael was so excessively alarmed that he left Goa, and his fear was much increased as some conjurer had foretold that he was to be killed by a cannon-shot near some river. He sent several ceremonious messages to Albuquerque, on purpose to discover what was doing on board the ships, and by the threatening answers he received his fears were materially augmented. In consequence of this intercourse of messages, Ismael was prevailed on to exchange some Portuguese, who had necessarily been left behind when Goa was abandoned; for the Moors engaged in the late conspiracy who remained prisoners with Albuquerque.

About this time Albuquerque received intelligence that some vessels were preparing at Goa to set his ships on fire, on which he anticipated the intentions of the Moors by sending a force up the river to burn these vessels, which was effected, but Don Antonio de Noronha was slain in this enterprise; Noronha used to moderate the violent passions of his uncle Albuquerque, who after his death allowed the severity of his temper to proceed to extremities. Having detected a soldier in an amour with one of the female slaves he used to call his daughters, and whom he was accustomed to give away in marriage, he ordered him immediately to be hanged; and as some of his officers demanded to know by what authority he had done this arbitrary and cruel deed, he ordered them all below deck, and flourishing his sword said that was his commission for punishing all who were disobedient, and immediately cashiered them all. During the continuance of this winter, the Portuguese fleet suffered extreme hardships, especially from scarcity of provisions; and on sailing from thence after the cessation of winter120, they discovered four sail which they supposed to have been Turks, or Mamelukes rather, but on coming nearer, they were found to be a squadron from Portugal under the command of Diego Mendez. Besides these, the king had sent out this year other seven ships, under Sequeira, who arrived at Cananor soon after Albuquerque; and a third armament of two ships to settle a trade at Madagascar.