The Portuguese were the first Europeans to come in significant numbers to the archipelago. The golden age of Portuguese exploration and conquest in Asia began with Vasco da Gama's voyage to India in 1497-99 and continued through the first half of the sixteenth century. Faith and profit, nicely harmoniÍÍÍÍzed, motivated these early European explorers. The papacy charged Portugal with converting Asia to Christianity. Equipped with superior navigational aids and sturdy ships, the Portuguese attempted to seize rich trade routes in the Indian Ocean from Muslim merchants. They established a network of forts and trading posts that at its height extended from Lisbon by way of the African coast to the Straits of Hormuz, Goa in India, Melaka, Macao on the South China coast, and Nagasaki in southwestern Japan. The Portuguese came to Indonesia to monopolize the spice trade of the eastern archipelago. Nutmeg, mace, and cloves were easily worth more than their weight in gold in European markets, but the trade had hitherto been dominated by Muslims and the Mediterranean city-state of Venice. Combining trade with piracy, the Portuguese, operating from their base at Melaka, established bases in the Maluku Islands at Ternate and on the island of Ambon but were unsuccessful in gaining control of the Banda Islands, a center of nutmeg and mace production.

Indonesian Muslim states wasted no time in trying to oust the intruders. During the sixteenth century, the sturdy Portuguese fort of A Famosa (the Famous One) at Melaka withstood repeated attacks by the forces of the sultans of Johore (the descendants of the ruler of Melaka deposed by the Portuguese), Aceh, and the Javanese north coast state of Jepara, acting singly or in concert. The Portuguese were minimally involved in Java, although there were attempts to forge alliances with the remaining Hindu-Buddhist states against the Muslims. The Portuguese goal of Christianizing Asia was largely unsuccessful. Saint Francis Xavier, a Spaniard who was an early member of the Society of Jesus (Jesuits), established a mission at Ambon in 1546 and won many converts whose lineal descendants in the early 1990s were Protestant Christians. The small enclave of Portuguese (East) Timor, which survived three centuries surrounded by Dutch colonialism only to be formally absorbed into Indonesia in 1976, was largely Roman Catholic.

Given Portugal's small size, limited resources, and small labor pool, and its routinely brutal treatment of indigenous populations, Portugal's trading empire was short-lived, although remnants of it, like Portuguese Timor, survived into the late twentieth century. Although numerically superior Muslim forces failed to capture Melaka, they kept the intruders constantly on the defensive. Also, the dynastic union of the Portuguese and Spanish crowns in 1580 made for Portugal a new and increasingly dangerous enemy: the Dutch.

Data as of November 1992