The potential for tree components of coffee agroforestry systems to provide ecosystem services is widely recognized. Management practices are a key factor in the amount and quality of ecosystem services provided. There is relatively abundant information on ecosystem services provision within agroforestry systems, but comparatively scant information regarding how coffee farmers manage their plantations, the factors influencing their farming practices and the extent to which farmers’ local knowledge – as opposed to global scientific understanding – underpins management decisions. Policymakers and scientists too frequently design development programs and projects in the coffee sector. On occasion technicians are included in the design process, but farmers and their knowledge are always excluded. This research explores farmers’ knowledge regarding how trees affect coffee productivity and ecosystem services in Costa Rica. Farmers’ knowledge on the effects of trees on coffee productivity was compared with that of other knowledge sources: coffee processors, technicians and scientists. Farmers were shown to have detailed knowledge regarding ecosystem services that their coffee agroforestry systems provide as well as on the interactions between trees and coffee productivity. When asked on the services that trees provide, farmers classified trees according to water protection, soil formation, or contribution to biodiversity conservation. These classifications were related to tree attributes such as leaf size, biomass production or root abundance. Comparison of coffee productivity knowledge from different knowledge sources revealed considerable complementarity and little contradiction.