Why did Islam and Christianity become the major religions in Indonesia? What are the historical roots of religious conflict in frontier zones in eastern Indonesia? The answers lie in a series of profound religious transformations in the long 16th century: the expansion of Islamic kingdoms, deep reformation within Hinduism and Buddhism, the infusion of beliefs and practices across religious boundaries, and vigorous debates about religious identity and orthodoxy. We lack an adequate theoretical model to understand these religious transformations, and there remain many empirical gaps in our knowledge of how these changes took place. This talk engages with neglected primary sources and the latest research to take the first steps towards an integrated account of religious transformation in the archipelago during this decisive time. It thus contributes to pressing conversations about religious identity and diversity in present-day Indonesia.