The objective of this study was to compare the carbon trade-offs of different coffee systems via quantification of carbon stock and greenhouse gas (GHG) emissions. Materials and methods Six coffee systems of shaded and unshaded (highly intensive, in terms of input use), shaded with exotic and native native trees (moderately intensive), and low and high shade tree density (least intensive) from Vietnam, Uganda and India, respectively, were compared. Carbon (C) stock was calculated from tree height, diameter, and wood density extracted from ICRAF database (http://db.worldagroforestry.org/wd) using allometric equations partly developed by Chave et al. (2014). GHG emissions were calculated from data on soils, fertilizer use, crop residues, energy use, and transportation of inputs and outputs using CoolFarmTool, an online GHG calculator (Hillier et al., 2011). Results and discussion The study showed that, higher carbon stock systems, did not significantly reduce Robusta coffee green bean yield (2.4 vs 2.6 tons ha-1 in shaded and unshaded coffee systems, Vietnam; 1.06 vs 1.04 tons ha-1 in shaded systems with exotic and native shade trees, India) while helped increase significantly carbon stock compared to unshaded systems (e.g., 15.2 tons carbon ha-1, Vietnam). The additional carbon was achieved by growing primarily with fruit trees in Vietnam (85 trees ha-1, contributing 15.2 tons C) and in India by maintenance of an agroforestry system with native shade trees (up to 245 trees ha-1, contributing 77.6 tons C) or exotic (Grevillea robusta) shade tree species (397 trees ha-1, contributing 47.5 tons C). The study also revealed that the GHG emission per unit product of systems in Vietnam (3.46 – 3.98 kg CO2e kg-1) are not significantly higher than those in India (3.09 – 3.13 kg CO2e kg-1), despite a much higher GHG emission per ha (7.5 vs 2.4 tons CO2e ha-1, respectively) resulted from a significantly (3-fold) higher application of inorganic fertilizers, the main GHG contribu