This 4‐year on‐farm study reports the effects of different agricultural practices on yield and soil organic carbon (SOC) in kiwifruit and apricot orchards grown in a Mediterranean area. Groups of plants under local orchard management (L_OM,§ ) practices (i.e. soil tillage, removing of pruning residues and mineral fertilisers) were compared with plots under soil‐protecting orchard management (SP_OM) actions (i.e. cover crop, no‐tillage, compost application and mulching of pruning residues). In the SP_OM blocks fertilisation rate was based on plant demand and irrigation volumes calculated on the evapotranspiration values, while they were empirically calculated in the L_OM plots. Results show that yield was 28–50 per cent enhanced by SP_OM practices while SOC remained close to the initial values. In comparison with L_OM plots, changed practices increased up to 28–90 per cent the amount of P and K, and 13 per cent that of N annually incorporated into soil increasing their reservoir in the soil. The study demonstrates that appropriate land management can increase the mean annual carbon soil inputs from about 1·5 to 9·0 t ha⁻¹ per year. Copyright © 2009 John Wiley & Sons, Ltd.