What explains when states strengthen, maintain, or erode political-territorial Indigenous autonomy regimes? Indigenous activists around the world have fought for the right to govern their own lands and communities and have sometimes won major legal concessions from national governments. Yet initial breakthroughs often give way to lackluster state implementation or even erosion of Indigenous autonomy rights. We examine how statebuilding incentives structure governments’ implementation of autonomy, drawing on cases in Central America. Under some circumstances government officials may perceive Indigenous autonomy regimes as the best option to promote state influence over otherwise difficult-to-reach territories and populations. Autonomy regimes may improve governability, for example, in regions where criminal organizations or other armed actors operate. Autonomy regimes may also lead Indigenous peoples to increasingly identify themselves with the national state. Finally, autonomy regimes may further integrate Indigenous communities into markets by creating property relations and consultation mechanisms that defuse Indigenous opposition to extractive projects. When these statebuilding incentives to advance governability, identification, and extraction are absent, however, government officials are more likely to erode autonomy regimes. Through comparisons of the trajectories of Indigenous autonomy regimes in Honduras, Panama, and Nicaragua, we show how these statebuilding concerns shaped state policies towards Indigenous autonomy across governments’ ideologies and regime types. Our findings highlight the importance of examining social movements’ practical consequences, and how aligning movement demands with statebuilding interests may shape whether gains can be defended and sustained, an especially pressing concern for Indigenous movements facing extractive projects, land invasions, and climate change.