Fruit tree orchards have a historical and economic importance for Mediterranean agriculture, notably in Spain. Fruit tree orchards have the potential to mitigate global warming by sequestrating carbon (C) and providing renewable fuels. Actually, there is few information on the benefits of organic practices. Therefore, we analyzed the greenhouse gas contribution of 42 pairs of organic and conventional perennial cropping systems, including citrus, subtropical trees, other fruit trees, treenuts, vineyards, and olives, using life-cycle assessment (LCA). The assessment was based on management information from interviews and involved the estimation of soil carbon sequestration, specific Mediterranean N2O emission factors, and the consideration of coproducts. Results show on average a 56 % decrease of greenhouse gas emissions under organic versus conventional cropping, on an area basis. On a product basis, greenhouse gas emissions decreased by 39 % on average. These findings are explained mainly by C sequestration in soils, which is due in turn to higher C inputs by cover cropping and incorporation of pruning residues.