Stateless nations in Indonesia have recently obtained self-determination rights in various forms of “special autonomy.” For several decades, nationalist movements in Aceh and Papua sought greater self-determination but were strongly repressed. When the Indonesian regime began to democratize in 1998, Acehnese and Papuan nationalist movements re-emerged even more strongly. In this paper, I compare how Acehnese and Papuans negotiated this constitutional transition. While the Acehnese obtained very detailed and extensive powers under the Law on Aceh, Papuans have repeatedly rejected the Special Autonomy Law that they obtained in 2001. Conflict in Aceh has largely subsided, while it continues in Papua. I argue that Indonesia’s incrementalist and responsive approach to constitutional change enabled a flexible and asymmetric accommodation of ethnic groups that has largely strengthened Indonesia’s stability and democratic character. Nevertheless, it reached its limits in Papua, where the state’s fear of secession fuels an overly defensive, and ultimately defeating approach.