This study evaluated the most significant physical, chemical and biological soil properties from a group of organic olive farms located in a typical olive-growing area of Andalusia, Spain, after 5 or more years since the shift from conventional to organic farming, and compared soils with those in nearby undisturbed (U) natural areas. Two soil management systems implemented in these organic olive farms to control weeds, tillage (T), characterized by non-inverting-shallow tillage in spring, and mechanical mowing (M), were compared and evaluated against the U areas. Organic olive orchards showed similar productivity (average fruit yield of 3130 kg ha−1 yr−1) as the conventional, rain-fed olive groves in the same area, with no significant differences due to soil management systems. Soil properties in the olive orchards (i.e. texture, pH, organic carbon (C), organic nitrogen (N), C:N ratio, cation exchange capacity (CEC) and exchangeable potassium) were in the suitable range for olive farming in both soil managements, although organic C and N, saturated hydraulic conductivity and available water-holding capacity (AWC) of the soil were lower than in the U areas. A principal component analysis (PCA) for soil properties in topsoil (0–10 cm depth) distinguished the T from M olive orchards and U areas, and determined organic C and N as the most significant soil properties to characterize them. Average values of soil organic carbon (SOC) stocks for the surface layer (0–10 cm depth) were 18.6, 59.3 and 67.8 Mg ha−1, for T and M soil management systems and U areas, respectively. This indicates that the sustainability of organic olive orchards could be significantly improved by shifting to M soil management to decrease soil erosion and depletion of SOC.