ABSTRACT To evaluate the effect of the management system on soil quality, chemical and biological properties were measured in soils (0–20 cm depth) from Japanese plum orchards managed under organic and conventional conditions. The experiment was conducted between 2005 and 2014 in orchards established at the agricultural research station at Alcalá del Río, Seville, Spain. Overall, the soil chemical parameters in the organic orchard showed higher concentrations of soil organic matter, total N, available P and Mg. There was a trend of higher concentrations of K and Na, though for these elements the differences were significant only in two and one years, respectively. Similarly, concentrations of Mn and Zn tended to be higher in the organic plots, whereas contradictory trends were shown for Fe and Cu. No differences were found between the treatments for other physicochemical parameters such as pH and electrical conductivity. Regarding soil biological properties, the organic system was characterised with a significantly greater abundance of bacteria and fungi compared with the conventional system. The rhizobia population and the legume biomass were also higher in the organic orchard and the plants had more nodules. Likewise, the number of earthworms was higher in the organic system. The results showed that long-term organic management, including the use of cover crops and compost, resulted in a significant shift of the chemical and biological characteristics of the soil compared with the conventional management practice, thus improving soil quality and suggesting that organic farming may provide a potential solution to achieve sustainable agricultural systems.