Indonesia, with its huge size (covering almost 2 million square kilometres), insular geography (spread out over some 17,000 islands), large population and linguistic ethnic diversity, is an arena predisposed to religious diversity and fragmentation. Islam arrived in the Indonesian islands in the thirteenth century, and by the sixteenth century had become the dominant religion, but this did not completely supplant pockets of older religions and practices like Hinduism and animism, especially in the more remote regions far away from the power base of the island of Java. The wealth of cash crops in the islands, especially spices like pepper and nutmeg, attracted the interest of the European colonial powers, including the Portuguese in the sixteenth century and the British for a brief period in the nineteenth century. However, it was the Dutch who exerted the most protracted colonial influence: after seizing Ambon in the Moluccas in 1605, the Dutch gradually extended their control over the Indonesian islands, bringing into subjugation the rulers of the different Indonesian kingdoms, and making treaties with rival colonial powers like the British.

As with the Malay Peninsula, Indonesia seems to have been visited by Christians from the Eastern Church, and some early Christian settlements on Sumatra and Java have been reported by various sources from the seventh to fifteenth centuries (Santoso 1996, p. 315). The rise of Islam from the thirteenth to fifteenth centuries also eclipsed these early Christian settlements. In the sixteenth century, the Portuguese brought Catholicism to parts of Indonesia; Francis Xavier's ministry in the Moluccas in 1546–47 did much to reinforce the acceptance of the religion in the eastern part of the islands (Santoso 1996, p. 315). However, when the Dutch established their dominance over the islands in the seventeenth century, they were as keen to suppress the old enemy of Catholicism.