Soil N2O emissions, soil N mineralization potentials and net carbon sequestration rates (difference between C sequestrated in the aerial biomass + litter and N2O effluxes expressed in CO2-equivalent) were estimated in coffee monocultures and coffee agroforestry systems (AFS) with N2 fixing legume shade trees, under two agricultural managements. One pair of coffee plots (unshaded and shaded coffee with Inga densiflora) was conventionally managed (250 kg N mineral ha-1yr-1); the other pair of coffee plots (unshaded and shaded coffee with Erythrina poeppigiana) was organically managed (150 kg N organic ha-1yr-1). In the conventional systems, N mineral fertilizer increased N2O emissions more intensively under the AFS than under the monoculture. Fertilizer-induced N2O emissions (FIE) was larger in the AFS (1.8% of the N applied) than in the monoculture (1.3% of the N applied). For both types of agricultural management, annual N2O emissions were larger under the AFS (5.8 and 3.7 kg N ha-1yr-1 for conventional and organic management, respectively) than under the monocultures (4.3 and 1.8 kg N ha-1yr-1 for the respective managements), confirming that N2 fixing legumes can increase N2O emissions. Larger N2O fluxes observed in the AFS compared to the monocultures were in agreement with larger soil N mineralization potential under the AFS. Despite that, net C sequestration rates were 3 and 5 times larger in the AFS than in the monocultures, under conventional and organic management, respectively. This implies that AFS are promising management practices to mitigate climate change.