He oversaw expeditions that resulted in establishing diplomatic contacts with the Ayutthaya Kingdom through his envoy Duarte Fernandes, with Pegu in Myanmar, and Timor and the Moluccas through a voyage headed by António de Abreu and Francisco Serrão.
They engaged in several battles against the forces of the Zamorin of Calicut (Calecute, Kozhikode) and succeeded in establishing the king of Cochin (Cohim, Kochi) securely on his throne.
After he assisted with the creation of a strategy for the Portuguese efforts in the east, King Manuel entrusted him with the command of a squadron of five vessels in the fleet of sixteen sailing for India in early 1506, headed by Tristão da Cunha.
[25] After successful attacks on Arab cities on the East African coast, the expedition conquered the island of Socotra and built a fortress at Suq, hoping to establish a base to stop the Red Sea commerce to the Indian Ocean.
[6] At Socotra, they parted ways: Tristão da Cunha sailed for India, where he would relieve the Portuguese besieged at Cannanore, while Afonso took seven ships and 500 men to Ormuz in the Persian Gulf, one of the chief eastern centers of commerce.
He ordered them to be given a stock of cannonballs, arrows and weapons, retorting that "such was the currency struck in Portugal to pay the tribute demanded from the dominions of King Manuel".
[6] In 1509, the nobleman Diogo Lopes de Sequeira was sent with a fleet to Southeast Asia, to seek an agreement with Sultan Mahmud Shah of Malacca, but failed and returned to Portugal.
Afonso rewarded him by appointing him chief "Aguazil" of the city, an administrator and representative of the Hindu and Muslim people, as a knowledgeable interpreter of the local customs.
In Goa, Afonso established the first Portuguese mint in the East, after Timoja's merchants had complained of the scarcity of currency, taking it as an opportunity to solidify the territorial conquest.
Upon hearing that the doctors were extorting the sickly with excessive fees, Albuquerque summoned them, declaring that "You charge a physician's pay and don't know what disease the men who serve our lord the King suffer from.
[43] Despite constant attacks, Goa became the center of Portuguese India, with the conquest triggering the compliance of neighbouring kingdoms: the Sultan of Gujarat and the Zamorin of Calicut sent embassies, offering alliances and local grants to fortify.
It was the richest city that the Portuguese tried to take, and a focal point in the trade network where Malay traders met Gujarati, Chinese, Japanese, Javanese, Bengali, Persian and Arabic, among others, described by Tomé Pires as of invaluable richness.
After fruitlessly waiting for the Sultan's reaction, they returned to the ships and prepared a junk (offered by Chinese merchants), filling it with men, artillery and sandbags.
To quell disagreements over the order of the names, he had it set facing the wall, with the single inscription Lapidem quem reprobaverunt aedificantes (Latin for "The stone the builders rejected", from David's prophecy, Psalm 118:22–23) on the front.
[46] He settled the Portuguese administration, reappointing Rui de Araújo as factor, a post assigned before his 1509 arrest, and appointing rich merchant Nina Chatu to replace the previous Bendahara.
[50] In November, after having secured Malacca and learning the location of the then secret "spice islands", Afonso sent three ships to find them, led by trusted António de Abreu with deputy commander Francisco Serrão.
Afonso returned from Malacca to Cochin, but could not sail to Goa as it faced a serious revolt headed by the forces of Ismael Adil Shah, the Sultan of Bijapur, commanded by Rasul Khan and his countrymen.
In a private letter to King Manuel I, he stated that he had found a chest full of books with which to teach the children of married Portuguese settlers (casados) and Christian converts, of which there were about a hundred, to read and write.
Mateus was sent by the regent queen Eleni, following the arrival of the Portuguese from Socotra in 1507, as an ambassador for the king of Portugal in search of a coalition to help face growing Muslim influence.
Socotra had proved ineffective to control the Red Sea entrance and was abandoned, and Afonso's hint that Massawa could be a good Portuguese base might have been influenced by Mateus' reports.
He attempted to reach Jeddah, but the winds were unfavourable and so he sheltered at Kamaran island in May, until sickness among the men and lack of fresh water forced him to retreat.
[56] Although Albuquerque's expedition failed to reach Suez, such an incursion into the Red Sea by a Christian fleet for the first time in history stunned the Muslim world, and panic spread in Cairo.
With peace concluded, in 1514 Afonso devoted himself to governing Goa and receiving embassies from Indian governors, strengthening the city and encouraging marriages of Portuguese men and local women.
In March 1514 King Manuel sent to Pope Leo X a huge and exotic embassy led by Tristão da Cunha, who toured the streets of Rome in an extravagant procession of animals from the colonies and wealth from the Indies.
In early 1514, Afonso sent ambassadors to Gujarat's Sultan Muzaffar Shah II, ruler of Cambay, to seek permission to build a fort on Diu, India.
He then had him immediately stabbed and killed by his entourage, thus "freeing" the terrified king, so the island in the Persian Gulf yielded to him without resistance and remained a vassal state of the Portuguese Empire.
[17] While on his return voyage from Ormuz in the Persian Gulf, near the harbor of Chaul, he received news of a Portuguese fleet arriving from Europe, bearing dispatches announcing that he was to be replaced by his personal foe, Lopo Soares de Albergaria.
As his death was known, in the city "great wailing arose",[67] and many took to the streets to witness his body carried on a chair by his main captains, in a procession lit by torches amidst the crowd.
[68] Afonso's body was buried in Goa, according to his will, in the Church of Nossa Senhora da Serra (Our Lady of the Hill), which he had been built in 1513 to thank the Madonna for his escape from Kamaran island.
[67] In Portugal, King Manuel's zigzagging policies continued, still trapped by the constraints of real-time medieval communication between Lisbon and India and unaware that Afonso was dead.