In Costa Rica coffee is an important crop with cultural values and covering an extensive land area. Coffee production is in a context where achieving production demands while still meeting resource conservation is becoming a challenge. Agroforestry systems (AFS) have been proposed as an alternative for land use providing a solution. However the inconsistency of coffee yields with or without shade depending as well on site conditions make the design of new adapted AFS necessary. Although agroforestry as a science is recent, its practices are old. Thus it is argued that gathering of local knowledge has an important role to play in agroforestry development. The study was held as part of the PCP project (Mesoamerican Scientific Partnership Platform) for Agroforestry Systems (AFS) with perennial crops. The project initiative aims at building a model to assist in the design of AFS with coffee. Research was Carried out in three districts of Costa Rica: Turrialba, Orosi and Tarrazú. The research objective was to build a biophysical conceptual model reflecting crop-environment interactions that occur in shade coffee crops, focusing on the variation of coffee productivity and quality. The conceptual model was founded on scientific, expert and farmer's knowledge about factors affecting coffee yield and quality elaboration. Semi-structured interviews with 42 persons were held on farms, technical institutes and coffee processing units. Interviews were entered on a knowledge base system, AKT (Agroecological Tool Kit). Outputs of the knowledge base as diagrams enabled the comparison of knowledge, from different sources, on processes and environmental factors affecting coffee yield and quality components. Comparison of farmers, experts and scientific knowledge revealed complementarities, with each knowledge system also providing added individual detail that did not contradict the other. In that way it was possible to propose for each component factors or processes that were not tak