Historical legacies of colonialism continue to shape the well-being of Indigenous People in Indonesia today. As other ethnic groups’ settlements expanded across Kalimantan and Papua, Indigenous nations were weakened by disease, environmental degradation, illegal occupation, and losing control over traditional territories and resources. These losses weakened a pre-existing sophisticated level of governance, spiritual practice, social cohesion, and culture. Over many decades, Indigenous peoples’ ongoing resistance to their lack of control and opportunity has eventually brought about some recognition and reparation for the systemic social, political, economic, and cultural discrimination they have endured due, in no small part, to successful court challenges and courageous traditional and contemporary leaders. The regional and local dimension is essential to Indigenous economic development because of Indigenous peoples' strong attachment in economic, social, cultural, and spiritual terms with traditional territories. Indigenous peoples in Kalimantan and Papua are likelier to live in predominantly rural regions lacking basic infrastructure and to experience poorer socio-economic outcomes. Gaps in well-being between Indigenous and non-Indigenous peoples are higher in rural interior areas than in urban coastal regions. This study identifies opportunities to improve the fairness and transparency for how Indigenous peoples can secure land tenure and use tools, such as land use planning, to promote community economic development as common prosperity. Indigenous entrepreneurship provides opportunities for Indigenous peoples to use assets and resources in ways that align with their objectives for development. Framework conditions for Indigenous rural entrepreneurship could be improved in digital connectivity and financial literacy areas. An approach to self-governance is needed that adapts policies to places and empowers Indigenous institutions and communities.