Terrestrial life forms rely on productive soils to provide a medium for plant growth and meet most of their nutrition needs. The aim of this study was to determine the variation in soil organic carbon stocks (SOCS), micro-arthropod communities, and physicochemical properties under different crop cover in Oshikhandas valley, Karakoram Range, Pakistan. Soil samples were collected from three depths under three different crop cover types, i.e., alfalfa, wheat and potato. Standard methods were used to analyze selected soil quality parameters and SOC. Berlese-Tullgren funnel method was used for the extraction of soil microarthropods. ANOVA results showed that physicochemical parameters were non-significantly variable between different crops. At different soil depths, bulk density (BD), pH, soil organic carbon (SOC), and SOCS were highly significantly (p<0.001) different, while moisture and electrical conductivity (EC) were non-significant. The highest value of SOCS was found under alfalfa (16.2Mg/ha) followed by potato (14.4Mg/ha), while it was lowest in wheat (12.2Mg/ha). Overall soil texture was silty clay loam and the soil was alkaline (pH 8.2). A total of 260 micro-arthropods were extracted and soil biological quality index (QBS-ar) was calculated. The predominant species were mites (61%) and Coleoptera (11%). The mean QBS index was highest in wheat (61.33) followed by alfalfa (55.66), and lowest in potato (43.66). The soil quality of the study area belonged to class 5 for wheat and 4 for Alfalfa and potato, which indicated good soil quality class. The highest population of micro-arthropod communities was seen in alfalfa (38%), followed by wheat (36%) and lowest in potato (26%). According to the results of the study, alfalfa is a good crop for improving soil biological health and acting as a carbon sink, so farmers should be encouraged to grow it for the long-term management of mountain agro-ecosystems.