The Portuguese introduced Catholicism to Indonesia, notably to the island of Flores and to what was to become East Timor. Protestantism was first introduced by the Dutch in the sixteenth century with Calvinist and Lutheran influences. Animist areas in eastern Indonesia, on the other hand, were the main focus Dutch conversion efforts, including Maluku, North Sulawesi, Nusa Tenggara, Papua and Kalimantan. Later, Christianity spread from the coastal ports of Borneo and missionaries arrived among the Torajans on Sulawesi. Parts of Sumatra were also targeted, most notably the Batak people, who are predominantly Protestant today.

Significant changes in religion aspect also happened during the New Order era. Following an abortive coup in 1965 officially blamed on the Communist Party of Indonesia, around 1/2 million were killed in an anti-communist purge. Following the incident, the New Order government had tried to suppress the supporters of PKI, by applying a policy that everyone must choose a religion, since PKI supporters were mostly atheists. As a result, every Indonesian citizen was required to carry personal identification cards indicating their religion. The policy resulted in a mass religion conversions, topped by conversions to Protestantism and Catholicism (Christianity). The same situation happened with Indonesians with Chinese ethnicity, who mostly were Confucianists. Because Confucianism was not one of the state recognised religions, many Chinese Indonesians were also converted to Christianity.