Although biodiversity has value for the global community, biodiversity protection often imposes costs on local communities. Correcting this misalignment requires appropriate local incentives. Conservation agreements (i.e. negotiated transactions in which conservation investors finance social benefits in return for conservation actions by communities) are a form of direct incentive. The results of this approach depend on effective monitoring of ecological and socio-economic impacts to verify that environmental and development objectives are met. Monitoring is also needed to verify that parties to the agreements comply with their commitments. Ecological monitoring results for agreements between Conservation International and communities in the Colombian Amazon show positive conservation impacts. These agreements are designed to protect forest areas and two threatened fish species that are important to local livelihoods and have high commercial value. We show how effective monitoring is essential for identifying long-term sustainability options. Lessons learned from this project inform reflection on emerging frameworks for scaling up the approach to the national level.