An energy analysis in orchards is useful to deciding best management strategies. The objective of this study was to evaluate, by selecting organic and conventional sweet cherry orchards located in/or close to Natura 2000 sites (a) the energy flow between the two farming systems and (b) the effect of farming system to gas emissions (CO2, CH4 and N2O). Twenty farms [(2-conventional and 2-organic) x 5-locations] were selected during 2003-2004. Means averaged over all locations for insecticides and fungicides application, fuel, insecticides, fungicides, non-renewable energy inputs, energy shoot outputs, energy fruit outputs, energy shoot + fruit outputs, fruit production, shoot efficiency, fruit efficiency, shoot + fruit efficiency, non-renewable energy efficiency, gas emissions were higher in conventional than in organic orchards, while fertilizer application, harvesting, fertilizers, labor, total energy inputs, renewable energy inputs, intensity and non-renewable energy consumption were higher in organic orchards. Means averaged over two farming systems for fertilizer, insecticide and fungicide application were higher in GRL2 and GRLS. The means averaged over two systems for transportation had the highest value in GRL4 and the lowest in GRL5. Finally, means averaged over two farming systems for labor had the highest value in GRL2. Non-renewable energy inputs as percent of total inputs were 82.63 and 52.42% in conventional and organic sweet cherry orchards respectively. The results show that organic farming systems could reduce non-renewable energy inputs and gas emissions in an efficient way in areas related to Natura 2000 sites. (C) 2010 Elsevier Ltd. All rights reserved.