A form of power-sharing, territorial autonomy is essential for managing separatism. Indonesia provides two non-Western cases to illuminate what makes autonomy work. In Aceh, autonomy helped to overcome conflict and can be regarded as successful, while in Papua, autonomy has failed, evident in continued unrest. Within the same country, the same institutional response to violent separatism has generated divergent self-government outcomes. Why has autonomy succeeded in Aceh, but failed in Papua? Utilizing within-case and temporal comparisons, we suggest that the content of autonomy may be less important than the process through which it unfolds. The powers granted to Aceh and Papua are similar, although how self-government was negotiated and whom it empowered varied. Early in Aceh and in Papua, autonomy was essentially imposed, empowering corrupt leaders, and sidelining dissidents. Aceh's ultimately successful autonomy was negotiated and saw popular former rebels take the reins of self-government.