The extent to which coffee agroforestry systems provide ecosystem services depends on local context and management practices. There is a paucity of information about how and why farmers manage their plantations in the way that they do and the local knowledge that underpins this. This research compares knowledge from coffee-growing areas bordering key forest reserves in Nicaragua, Costa Rica and Guatemala. Knowledge was acquired from over 170 farmers in a stratified purposive sample, using established knowledge based systems methods. Farmers in all 3 countries had detailed knowledge about how trees affected ecosystem services such as soil formation, erosion control, provision of wildlife habitat and water conservation. Links between trees and biodiversity, pollination, biological pest control and micro-climate regulation were understood, and species were classified according to their role in both providing and regulating services. Trees were said to produce ‘fresh’ shade that was suitable for coffee or ‘hot’ shade that was not suitable. This was explained in relation to leaf texture and size; foliage density, crown shape and root system attributes. Much of the local knowledge about how trees could improve provision of ecosystem services, however, was not practically applied because farmers were concerned that increasing levels of shade would decrease yields. A range of trees and shrubs were maintained in coffee plantations at all sites but different tree species were dominant and diversity varied two-fold amongst sites. The degree of shade tolerated was the main difference across countries and this was strongly related to socioeconomic factors such as the prevailing demand for fuelwood. Comparative analysis allowed us to identify generally applicable knowledge across sites as well as the key factors that determine how knowledge was locally applied