Albuquerque also understood the necessity of establishing a base of operations in lands directly controlled by the Portuguese crown and not just in territory granted by allied rulers such as Cochin and Cannanore.

Marshal of Portugal Dom Fernando Coutinho had been killed in Calicut, fortuitously leaving Albuquerque with full, uncontested command of Portuguese forces in India.

[9] By the Mount of Eli, Albuquerque summoned his captains to his flagship Flor de la Mar, where he revealed the objective of the expedition: He had orders from King Manuel I to subjugate Hormuz, but seeing as the Mamluks were assembling a fleet at Suez, he considered diverting from the original course of action to destroy it before it was ready.

At Pangim, Albuquerque received envoys from the most important figures of Goa, and proposed religious freedom and lower taxes if they accepted Portuguese sovereignty.

[15] In the city, the Portuguese found over 100 horses belonging to the ruler of Bijapur, 25 elephants, and partially finished new ships, confirming Timoji's information about the enemy's preparations.

[19] At the same time, Albuquerque sent friar Luiz do Salvador ahead of an embassy to the court of the neighbouring Hindu Vijayanagara Empire, hoping to secure an alliance against Bijapur.

Ismail then set up his royal tent by the Banastarim ford, waiting for the monsoon to trap the Portuguese before giving Pulad Khan the order to assault the island.

[citation needed] Albuquerque was informed of this plan through the Portuguese renegade João Machado,[21] who was now a prestigious captain in Ismail's service, though he remained Christian.

Under these conditions, Pulad Khan launched a major assault on May 11, across the Banastarim ford at low tide amidst a heavy storm, quickly overwhelming the small number of Portuguese troops.

Albuquerque refused to set fire to the city since this would announce their retreat to the besiegers and instead ordered a great quantity of spices and copper to be scattered on the streets to delay the enemy's advance.

Before leaving however, he had Timoji with fifty of his men execute the Muslim inhabitants within the citadel, but also took several women that had belonged to Adil Khan's harem onto his ship, to later offer them as maids-in-waiting to Queen Maria.

[citation needed] The governor would run through every ship, raising morale and instilling discipline, but his relation with his captains was degrading rapidly after his popular nephew, Dom António de Noronha, died in a sortie on land.

With the noose around his neck, mutiny sparked among the ranks of Portuguese fidalgos in the armada – who objected not so much to his execution but the fact that he was being hanged and not beheaded as befitted a fellow nobleman.

[34] Before leaving for Goa, Albuquerque was alerted by the Raja of Cochin, a faithful ally of the Portuguese, of an impending power dispute between him and his cousin and requested his assistance.

[35] At Honavar the Portuguese once more joined forces with Timoji, who informed Albuquerque that Ismail had left a considerable garrison behind, about 8,000–10,000 "whites" (Persian and Turkic mercenaries) supported by native infantry.

[34] On November 24, the Portuguese again sailed into the Mandovi and anchored by Ribandar, where they landed some men commanded by Dom João de Lima to scout the city's defences.

Once ashore, the heavily armoured Portuguese infantry, led by the steel-clad fidalgos of the squadrons of Vasconcelos and Lacerda, assaulted the outer defences around the riverside gates.

In a last-ditch effort to organize a defence, some of the defenders rallied around the palace of Ismail Adil Shah, but they too were eventually shattered by a second Portuguese assault commanded by Vasconcelos, arriving at the sound of trumpets.

[37] After five hours fighting, the defenders were now in a definitive rout, fleeing across the streets and away from the city along with many civilians – many of whom drowned trying to cross the narrow bridge over the moat in the ensuing flight, or were chased down by the Hindus of Goa.

[37] The Portuguese suffered 50 dead and 300 wounded in the attack – mainly due to arrows – while Albuquerque estimated that about 800 "Turks" and over 6,000 "moors" among civilians and fighting men had perished.

[40] It was garrisoned with 400 Portuguese soldiers, while a corps of 80 mounted crossbowmen served as watchmen and gateguards of the city, commanded by the captain of Goa, Rodrigo Rabelo, who received a bodyguard of 20 halberdiers.

[41] Timoji regained his post as tanadar-mor but his lowly caste as well as his mistreatment of underlings caused tensions within the Hindu society, and so he was replaced with his rival Melrao (Madhavrav), who had at his disposal 5,000 men to assist with the defence.

[41] With an effective defensive system in place, Diogo Mendes de Vasconcelos requested the governor's permission to proceed to Malacca, which Albuquerque refused.

Albuquerque ordered eight ships to destroy the stockade; once this was achieved, the vessels moved on ahead of Benastarim, thus blockading it from the river side, and initiated a naval bombardment.

[56] While keeping his word, their fates would prove to be worse than death: for having abandoned their comrades in combat, turned against them, and converted to "infidel" faith, Albuquerque decreed that they be punished by public mutilation, before a crowd in the main square.

[63] Establishing a strong naval base at Goa furthermore served a vital part in Albuquerque's strategy of undermining Muslim trade in the Indian Ocean, as Portuguese naval forces could then sever the link between the hostile Sultanate of Gujarat and the rich spice-producing regions in Southern India and Insulindia, where powerful Gujarati communities of merchants could be found, inciting local rulers to attack the Portuguese.

[citation needed] Arguably, what became Albuquerque's most iconic policy was that of encouraging his men to take local wives and settle in the city, granting them land confiscated from the evicted Muslims and a dowry provided by the state.

Nonetheless, the practice continued well beyond Albuquerque's lifetime, and in time the casados and the Indo-Portuguese descendants would become one of the Crown's main reserve of support whenever insufficient men and resources arrived from Europe.

[68][69] His tomb at the Nossa Senhora da Serra hermitage was converted to a shrine by the local Hindus, who would leave flowers there in his dedication and direct prayers to him, seeking aid in matters of justice, until his remains were returned to Portugal in 1566.

[citation needed] In 1526 King John III granted the city of Goa and its town hall the same legal status as Lisbon, in a foral in which the general laws and privileges of the city, its town hall, and the local Hindu community were detailed – especially important since at the time the native laws of Goa were still not written, instead being handled by councils of elders or religious judges and passed down orally (thus prone to abuses).