Interspecific grafting of Coffea arabica scions on C. canephora rootstock has been proposed as a strategy against nematode infestation, but also for cultivation of coffee under environmental stressors (such as temperature extremes). An agroforestry-like microclimate was established using artificial shade nets (30% light interception) across a multi-site elevation trial (from 1000 to 1450 m above sea level) in Costa Rica (Alajuela region). The effects of interspecific grafting of scions from modern C. arabica varieties ('Villa Sarchi' and an F1 hybrid called 'H3') onto C. canephora ('Nemaya') rootstock were tested under these conditions. The interactions between grafting, genotype and elevation were determined on the above- and below ground growth, agronomic traits, photosynthesis as well as bean and cup qualities. Variation in the protuberance of the graft union (trunk vs. below graft union collar diameters) were detected. However, no physical vascular blockages were observed in any of the interspecific grafted plants. Generally, interspecific grafting negatively affected most aerial and root traits as well bean yields for both 'H3' and 'Villa Sarchi' varieties compared to the non-grafted plants. A significant reduction in the photosynthesis of grafted 'H3' (in terms of Vcmax and FCO2max) was also observed. However, there were no impacts of grafting on the final bean attributes nor cup quality. Genetics of the scions largely determined coffee yields, with higher yields produced by 'H3' compared to 'Villa Sarchi'. The scion also controlled agronomic traits, bean qualities and belowground biomass (dry weight of taproot, secondary root mass and overall root system). This was observed when either C. arabica or C. canephora scion material was used. Increasing elevation significantly reduced the trunk, branches and shoot system, chlorophyll fluorescence parameters and other agronomic traits. However no significant interactions were found between grafting and elevation (wi