This article critically examines engagements of village leaders in an NGO-facilitated participatory conservation program in eastern Indonesia. It explores how the program’s implementation strengthened leadership legitimacy of a dominant customary social group. Customary leaders ensured distribution according to particular norms, and in organizing village governance upheld specific interests and claims over natural resources. Villagers outside of the customary group remained marginalized in village governance, despite being important stakeholders. Findings reveal complex relationships between leaders and villagers that were strongly framed by orders of power and cultural history, which influenced how and to what extent peripheral groups participated. The case study concludes that village leaders can form effective avenues to deliver on conservation outcomes. However, in their preoccupation with maintaining leadership legitimacy, they may inadequately address dynamic intra-community tensions that could jeopardize long-term outcomes. Co-management partners can play significant roles in adapting management and prompting more inclusive governance processes.