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Evaluation and monitoring are critical to agroforestry (AFS) project management, especially if they aim to contribute to use and conservation of biodiversity and plant genetic resources. A methodology to analyze information used in decision-making processes was developed and applied in a biodiversity conservation project in the Brazilian Amazon. Quality of information gathered at landscape, AFS, species (Bactris gasipaes Kunth, both wild and cultivated varieties) and genetic diversity levels in three dimensions was analyzed. The information at the landscape level was good, while that in the organizational-institutional and socio-economic dimensions was acceptable; information gaps were serious in the genetic-ecological dimension. Ecological and economic functionality assessment based on indicators built upon reported administrative actions suggests that information related to conservation played a greater role in decision-making and management than information associated with use and development. The application of the methodology proved instrumental for enhancing efficacy of decision-making within an adaptive management approach to plant genetic resources use and conservation.