Soil fauna abundance and diversity and organic matter content are key indicators for the rate of soil degradation in Mediterranean-type ecosystems. The soil macrofauna populations were examined in three orange (Citrus sinensis) orchards and one persimmon (Diospyros kaki) orchard, with the same soil type and different management systems, to establish whether organic management benefits soil fauna and soil quality and what is the effect of flood irrigation. Vegetation cover, soil organic matter, bulk density and moisture were measured at each experimental site within the Canyoles watershed in Eastern Spain in summer of 2015. Earthworm abundance was highest at the organic orchard with flood irrigation, followed by the organic orchard with drip irrigation, with juvenile endogeic earthworms being the dominant group. Soil isopoda was the dominant group of the arthropod macrofauna, with highest abundance in the drip-irrigated organic orchard. Earthworm presence was highest in the flood-irrigated orchard, whereas soil arthropoda abundance was highest at the drip-irrigated organic site, where a thick litter layer was present. The soil organic matter was higher and soil bulk density lower at the organic orchards sites compared to conventional ones. The results suggested that organic farming was beneficial for soil biological activity, though the conversion from flood to drip irrigation can have a negative impact on earthworms, which may cause a decrease in infiltration capacity of the soil.