Conventional, intensively managed coffee plantations are currently facing environmental challenges. The use of shade trees and the organic management of coffee crops are welcome alternatives, aiming to reduce synthetic inputs and restore soil biological balance. However, little is known about the impacts of the different types of shade tree species on soil functioning and fauna. In this paper, we assess soil nutrient availability and food web structure on a 17-year old experimental coffee plantation in Turrialba in Costa Rica. Three shade types (unshaded coffee, shaded with Terminalia amazonia, and shaded with Erythrina poepiggiana) combined with two management practices (organic and conventional) were evaluated. Total C and N, inorganic N and Olsen P content, soil pH, global soil fertility, and nematode and microarthropod communities were measured in the top 10¿cm soil layer, with the objective of determining how shade tree species impact the soil food web and soil C, N and P cycling under different types of management. We noted a decrease in soil inorganic N content and nematode density under conventional management (respectively -47% and -91% compared to organic management), which suggested an important biological imbalance, possibly caused by the lack of organic amendment. Under conventional management, soil nutrient availability and fauna densities were higher under shade, regardless of the shade tree species. Under organic management, only soils under E. poeppigiana, a heavily pruned, N2-fixing species, had increased nutrient availability and fauna density, while T. amazonia shade had a null or negative impact. The effects of coffee management and shade type on soil nutrient availability were mirrored by changes in soil food web structure. Higher fertility was recorded in soil with balanced food webs. These results emphasize the importance of the choice of shade tree species for soil functions in low input systems, more so than in fertilized systems.