Agricultural practices can play an important role in atmospheric CO2 emission and fixation. In this study, we present results on carbon fluxes in the biomass of two typical Mediterranean orchards indicating that proper canopy management coupled with other agricultural techniques could increase the absorption of atmospheric CO2 and its storage. We also discuss the potential environmental contribution of the orchards to enhancement of both soil and air quality. Trials were carried out in southern Italy on olive (Olea europaea L.) and peach orchards (Prunus persica L.) at different age and plant densities. At the end of each vegetative season, values of fixed atmospheric CO2 were calculated by measuring dry matter accumulation and partitioning in the different plant organs. In the early years, sequestered CO2 was primarily distributed in the permanent structures and in the root system while in mature orchards the fixed CO2 was distributed in leaves, pruning materials and fruit. Significant differences in amounts of fixed CO2 were observed in peach orchards cultivated using different planting and training strategies. The results underline the importance of training system, plant density and cultivation techniques in the absorption of atmospheric CO2 and its storage as organic matter in the soil.