Vegetation degradation can have significant effects on organic matter fractions as well as various soil characteristics. All these can lead to the changes in soil microbial communities, which are main drivers of nutrient cycles. This is especially important for mountainous ecosystems that are very sensitive and fragile habitats due to their climatic conditions, but less attention has been paid to them. Thus, Mirkola mountainous region (northern Iran) with semi-arid climate and vegetation being dominated by Crataegus and Berberis shrubs were investigated in this study. Sites with different intensities of vegetation degradation [light (60–70 % coverage), moderate (30–40 % coverage) and heavy (0–10 % coverage)] and also non-degraded control sites (90–100 % coverage) were selected. In order to avoid pseudoreplication, three plots, each with an area of 1 ha (100 m × 100 m), were used for each of the four studied habitats. Soil (in three soil depths at 0–10 cm, 10–20 cm and 20–30 cm) samples were collected from the corners and also the center (n = 5) of the plots using iron frames (30 × 30 cm). A total of 180 soil samples (4 habitats × 15 sample × 3 depths) were transferred to the laboratory. Labile and non-labile contents of soil organic matter (SOM) (C and N in soil particles and aggregates, C and N stocks, particulate and dissolved organic matter, hot-water extractable carbohydrate, C and N mineralization) were measured in each of these sites. Results showed that vegetation degradation might result in both labile and non-labile SOM losses. SOM and its associated properties were highest in the non-degraded sites, whereas, lower values were common under degraded areas. Based on the obtained data, vegetation cover can enhance the amount of organic matter entering the soil (especially in the surface layers) and formation of fertile islands in ecosystems. Accordingly, vegetation protection is emphasized to maintain stability and provide ecosystem services in mountainous semi-arid regions.