For programs that aim to promote forest conservation and poverty alleviation, such as Reducing Emissions from Deforestation and Forest Degradation (REDD+), the participation of indigenous communities is essential to meet program goals. Using Ostrom’s theory of collective action for common-pool resource management, we evaluated the institutions governing indigenous participation in the Programa Socio Bosque incentive-based conservation program in Ecuador. We conducted structured interviews with 94 members in 4 communities to assess community institutions for 6 of Ostrom’s principles, using 12 measures we developed for the principles. We found substantial variation between communities in terms of their institutional performance. The best-performing community performed well (>50% of interviewees reported successfully meeting the measure) on 8 of the 12 measures. The weakest performed well on only 2 out of 12 measures. Overall, our results indicate that there is a stronger performance for constitutional-level institutions, which determine who gets to make the rules, and some collective-choice institutions, which determine how local rules are made. We identified specific challenges with the day-to-day operational institutions that arise from participation in nation-state–community conservation programs, such as restricted resource appropriation, monitoring and compliance, and conflict resolution. We found that top-down policy-making has an important role to play in supporting communities to establish constitutional-level and some collective-choice institutions. However, developing operational institutions may take more time and depend on local families’ day-to-day use of resources, and thus may require a more nuanced policy approach. As some countries and donors find a jurisdictional REDD+ approach increasingly attractive, complementing top-down policy measures with bottom-up institutional development could provide a stronger platform to achieve the shift from current land use driving deforestation to a lower-carbon emissions land management trajectory.