Partitioning of gross rainfall into throughfall, stemflow and rainfall interception was assessed in Costa Rica during two rainy seasons (mean annual rainfall of 2900 mm) in two coffee systems: (1) a monoculture (MC) and (2) an agroforestry system (AFS) including Inga densiflora as the associated shade tree species. Coffee architecture, not LAI, appeared to be the main driver of stemflow as stemflow was higher for shaded coffee plants (10.6% of incident rainfall) than for coffee plants in MC (7.2%), despite the fact that these shaded plants had lower LAI. The presence of Inga trees modified coffee architecture with shaded coffee plants presenting larger stems and branches resulting in higher coffee funneling ratio under shade. In AFS, coffee plants and trees accounted respectively for 88% and 12% of total stemflow which represented 11.8% of incident rainfall. AFS displayed larger cumulative stemflow and smaller total throughfall compared to MC. Cumulative throughfall expressed in % of the gross rainfall, differed between systems and monitoring periods and the trend showed a decrease with increasing LAI. Nevertheless, as stemflow measurement and interception loss estimation were done only during the second year of the study, the shade tree showed a low influence in increasing interception loss, as the combined LAI of coffee plants and shade trees was rather similar in AFS as that of coffee in MC. Furthermore, coffee plants accounted for the largest fraction of the interception loss in AFS as the coffee LAI was more than 3-fold that of shade trees.