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This paper aimed to analyse and compare the environmental and energy sustainability of two orchards (peach versus kiwifruit) located in Southern Italy using Life Cycle Thinking. To this end, anthropogenic energy, CO2 emissions, biogenic energy and carbon gains were also considered through Life Cycle Assessment methodology and Energy Analysis. The C–CO2 balance was calculated as the difference between total C–CO2 stored in soil and trees, at the end of their life cycles, and orchards Carbon Footprint (CF). The results showed that the production of 1 kg of peaches caused minor impacts, especially with reference to CF (0.124 kg CO2 eq against 0.145 for kiwifruit), while it required 1.56 MJ of energy against 1.32 MJ for kiwifruit. In both orchards the main sources of direct CO2 emissions came from fuel combustion, nitrous oxide release by crop residue decomposition, and nitrogenous fertilizer distribution. Nevertheless, both orchards had sustainable environmental and energy results. Despite the management of the orchards releasing CO2 and consuming energy, they showed a significant capacity to store CO2 and energy, proving to be virtuous systems. This research can give useful indications for farmers, farmer associations, technicians, and stakeholders to improve orchard management efficiency. The net balance approach seems to be an adequate strategy, allowing best estimation of environmental impacts and guiding farmer decisions towards more sustainable alternatives.