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A Bayesian belief network (BBN) was developed to assess preferred combinations of trees in live fences and on pastures in silvopastoral systems. The BBN was created with information from Rivas, Nicaragua, using local farmer knowledge on tree species, trees' costs and benefits, farmers' expressed needs and aspirations, and scientific knowledge regarding tree functional traits and their contribution to ecosystem services and benefits. The model identifies combinations of trees, which provide multiple ecosystem services from pastures, improving their productivity and contribution to farmer livelihoods. We demonstrate how the identification of portfolios of multifunctional trees can satisfy a profile of desired ecosystem services prioritized by the farmer. Diagnostics using Bayesian inference starts with an identification of farmer needs and ‘works backwards’ to identify a silvopastoral system structure. We conclude that Bayesian belief networks are a promising modeling technique for multi-criteria decisions in farm adaptation processes, where interventions must be adapted to specific contexts and farmer preferences.