Deforestation and forest degradation in the Peruvian Amazon represent a major threat to biodiversity-related ecosystem services and the global climate. In 2010, the Peruvian Ministry of Environment launched the National Forest Conservation Program for Climate Change Mitigation, an innovative approach to maintaining forest cover of over 54 million hectares of land in protected areas and indigenous and peasant communities. A key component is a payments for environmental services scheme encouraging investments in sustainable land and forest uses in community-controlled territories. We conducted an ex-ante assessment of how the program would play out in terms of conservation cost-effectiveness, income effects and distributional (equity) outcomes if payments were up-scaled, as intended, to all native communities in the Peruvian Amazon. Our spatially explicit impact assessment relied on remotely sensed deforestation data and field data-supported estimates of conservation opportunity costs. We found that the spatially heterogeneous distribution of forestland and economic returns to multiple land uses across communities results in important tradeoffs between hypothetical cost-effectiveness, poverty alleviation and equity outcomes. Nevertheless, our scenario analyses suggested that alternative design options for payment schemes could improve both cost-effectiveness and equity outcomes simultaneously.