Some very broad-strokes comparisons can be made, given that people of Chinese descent have historically often been negatively stereotyped as a wealthy, economically-dominant ethnic minority in the archipelago.

People of mainland Chinese ancestry have lived in the Indonesian archipelago since at least the 13th Century. While they are conflated by some as a homogenous group, they of course are not. There were many different waves of migration and groups from many different ethnic and cultural backgrounds originating from what is now China but was historically the domain of lots of different peoples and empires.

Regarding how people of Chinese ancestry have been treated in Indonesia, consider that the notion of a national Indonesian identity didn't exist before the early 20th century. People of mainland Chinese descent always represented small minorities in the archipelago, but, there would have been a myriad of different experiences depending upon where one was and what one's status was. Consider the strong trade links between the archipelago and mainland Asia, and the broad variety of peoples who would've mixed in the major ports. In modern times, people of Chinese ancestry often owned and operated stores, restaurants and other local businesses throughout the archipelago.

Chinese Indonesians were discriminated by law from the 1950s, increasing greatly under Suharto, from the mid-1960s. In the early 1950s the Government of Indonesia implemented the Benteng (fortress) program), under which only native Indonesians were allowed licenses to import certain items. Illicit business activities between Chinese and native Indonesians nevertheless took place, often arrangements involving native Indonesians fronting a Chinese-owned business to circumvent these laws. This became known as 'Ali Baba', Ali being a common Muslim name and Baba referring to the Chinese.

In the 1960s, a range of legislative changes under Suharto sought to combat what they now termed 'the Chinese problem'. These changes largely sought to assimilate (rather than integrate) the Chinese population into Suharto's Pancasila Democracy, by oppressing the notion of a cohesive Chinese ethnic identity in Indonesia. The expression of Chinese culture through language, religion, and traditional festivals were, for the most part, banned. Ethnic Chinese were even pressured to adopt Indonesian-sounding names. During this period, the negative stereotyping of Chinese Indonesians increased greatly.

Social policy reforms since 1999, after Suharto's ousting, have sought to reverse cultural discrimination against Chinese Indonesians, but some division and prejudice lingers on.