Soil plays an essential role in providing ecosystem services, especially in mountain ecosystems which are often considered as fragile and sensitive systems. Crataegus is distributed in wide areas of mountain semi-arid regions of the world. Despite the importance of the presence of this plant in creating a cover for soil protection and nutrient cycling, the role of the shrublands dominated by Crataegus, and shrublands consisting Crataegus and other shrub species on soil function indicators, i.e. fertility and biological activities, has not been investigated. In this study, shrublands of four different species composition [i.e., Crataegus melanocarpa M. B., Berberis integerrima Bunge., Ribes Uva – crispa L. and Prunus spinosa L. (CM-BI-RU-PS); Crataegus melanocarpa M. B., Berberis integerrima Bunge and Ribes Uva – crispa L. (CM-BI-RU); Crataegus melanocarpa M. B. and Berberis integerrima Bunge (CM-BI), and Crataegus melanocarpa M. B. (CM)] on different soil properties in northern Iran was considered. For the analysis of soil physical and chemical characteristics, from each of these shrublands, 15 samples from soil surface layers (0–10 cm depth in 30 × 30 cm area) were taken. In addition, soil samples from the subsurface soil (10–20 cm depth) were also taken in order to calculate the ratio of organic matter stratification. Also, the population of soil fauna and flora were investigated in the middle months of each season. Based on the output of two-way analysis indicates that season is the main and primary factor in explaining the changes in epigeic density/biomass, anecic density/biomass, and total earthworm density/biomass. In contrast, the variability of endogeic density/biomass, Acarina, collembola, nematode, protozoa, fungi and bacteria densities was more influenced by the shrublands effects. Principal component analysis showed that the higher values of organic matter stratification, fertility and populations of soil biota, are assigned to the CM-BI-RU-PS and CM-BI-RU. In contrast, the least values of these soil characters belong to CM-BI and CM shrublands. Our findings indicated that the stand composition of the Crataegus can affect soil function indicators due to the change in the litter turnover time and different physical and chemical characteristics of the soil. In this regard, it is recommended that other shrubs (in the form of mixed vegetation) be used in addition to planting Crataegus for the restoration of degraded areas with similar climatic conditions.