Recent European incentive policies clearly targeted decreasing pesticide use in all agricultural systems as a key option to reduce environmental hazards and health risks. To reduce pesticide use is challenging in orchards where pesticides are recurrently applied to control numerous pests and diseases, but crucial to improve fruit production sustainability. Agricultural research has provided alternatives to chemical control for the management of a single pest or disease, but has very seldom addressed the design of overall sustainable strategies aiming at reducing pesticide use. New insights permitted by system approaches are now developing. Here, we report the level of pesticide use and the agri-environmental performances of three protection systems of apple orchards surveyed from 2005 to 2008: (1) conventional, (2) low-input and (3) organic farming. To assess the significance of the cultivar in decreasing pesticide use, these protection systems were combined with three cultivars differing in scab susceptibility: ‘Ariane’ (Vf-resistant), ‘Melrose’ (low-susceptibility) and ‘Golden Delicious’ (susceptible). Thus, nine ‘management × cultivar’ apple orchard systems were assessed. The level of pesticide use was the highest in conventional ‘Golden Delicious’ and in ‘Golden Delicious’ plots whatever the protection system. A 43–56% decrease in pesticide use was observed in ‘Ariane’ and ‘Melrose’ in both low-input and organic farming protection systems compared to conventional ‘Golden Delicious’ as reference. Only low-input ‘Melrose’ and low-input ‘Ariane’ systems achieved a level of yield and fruit damages similar to the corresponding conventional cultivars under reduced pesticide use, also permitting reduced environmental impacts. But even the low-input ‘Melrose’ least pesticide-dependant system was far from being pesticide-free, suggesting that current straight-designed mono-clone orchards are hardly appropriate to drastically reduce pesticide use and that the range of commercial apple cultivars should be renewed to offer more robust cultivars