The temporal and spatial dynamics of soil fauna in many terrestrial ecosystems are still not fully understood, while soil fauna is one of the most critical characteristics in assessing soil quality. Therefore, the effects of native [Quercus brantii (QP) and Amygdalus scoparia (AMP)] and non-native [Cupressus arizonica (CUP) and Pinus eldarica (PIN)] plantations and natural trees [Quercus brantii coppice trees (QNC), standard (QNS), and Amygdalus scoparia (AMN)] on diversity and abundance of macro- and mesofauna were done in the semi-arid forest of Zagros, Iran. Samples were collected beneath the canopy of woody species and the outer edge of the canopy in spring and summer seasons. For this purpose, soil samples [(7 samples per woody species + control) × 2 seasons × 3 replicates] were taken from 0 to 20 cm depths. Each soil sample was a mix of three soil cores. For the macrofauna, 15 species belonging to four families (in spring) and 17 species in nine families (in summer) were collected and identified. For the soil mesofauna, 14 species belonging to 14 families (in spring) and 13 species in 13 different families (in summer) were identified, respectively. The fauna diversity indices under the canopy of studied species were higher in summer season than in spring. The result showed that the macrofauna diversity was affected by tree species, while mesofauna was affected by seasonal changes. Macrofauna biodiversity was higher under the canopy of PIN and CUP than other trees. Principle component analysis showed that the diversity of the macrofauna was higher under the canopy of PIN and CUP, and influenced by soil characteristic properties, soil properties did not influence them. Yet the diversity of the mesofauna was affected by soil characteristics and was higher in areas with higher organic carbon, nitrogen, substrate-induced respiration, basal respiration, microbial carbon biomass, and alkaline phosphatase. In addition, mesofauna biodiversity had a significant positive correlation with the soil quality index (SQI). SQI was higher under the canopy of natural stands, especially the QNS. Conservation of native species (QNS, QNC, and AMN) and plantation with native deciduous species (QP and AMP) seem to moderate environmental conditions and increase soil macro- and mesofauna diversity and SQI.