Although the conventional farming system (CV) for apple production remains the common practice worldwide, the organic farming system (OF) is becoming increasingly important. Few global assessments of the environmental impacts of organic orchard systems are currently available. In this work, we analyse the weak and strong points of the environmental performance of the growing phase of two organic and one conventional apple orchard, using a pluri-annual dataset from experimental orchard systems located in the Middle Rhone valley in France, with life cycle analysis (LCA). LCA, also referred to as cradle-to-grave analysis, allows a quantitative and global evaluation of an orchard’s environmental performance. The analysis was performed using the SALCA (Swiss Agricultural Life Cycle Assessment) method (SALCA-Crop V3.1, adapted for pome fruit) and included relevant impact categories based on characterisation models derived mainly from the EDIP97 and CML01 methods, as well as those developed by Agroscope (ART). Seven impact categories that included ecotoxicity and human toxicity, as well as energy consumption and other environmental impact categories, were calculated and are discussed here. The OF systems appeared to have less of an impact than the conventional system, considering the surface-based functional unit (ha/year). However, the basic substitution of conventional with organic inputs or mechanised activities was not sufficient to radically improve the overall environmental performance of the orchard systems. These results need several years of full production to be validated.