In the rugged landscape of the Karakoram Range in lower Hunza Pakistan, we examined the agricultural soil quality under conventional and organic farming systems. Soil samples were collected from both farming practices using quadrates of 10*10 cm² at a depth of 0-10 cm for both physico-chemical and microarthropods extraction.The modified Berlese funnel method was used to extract soil microarthropod communities. The Soil Biological Quality Index (QBS-ar), Population Density (PD), and Taxa Richness (TR) were determined. Multivariate analysis of variance (MANOVA) showed a significant variation between conventional and organic farming systems for pH while most of the investigated parameters like bulk density (BD), moisture, soil temperature, Soil organic carbon (SOC), Soil organic matter (SOM), Nitrate nitrogen (NO₃-N₎, Available Phosphorus (Av. P), Exchangeable Potassium (Ex.K), QBS-ar, Population density, and Taxa richness did not show significant differences, however, the mean value of BD, PD, TR, and moisture were higher at organic farming while soil temperature, pH, Electrical conductivity (EC), SOM, SOC, NO₃-N, Ex. K and Av. P were higher in the conventional farming system. Pearson Correlation showed a significant negative relationship of EC with SOM, SOC, QBS-ar, and TR. In contrast, TR has shown a positive correlation with SOC, SOM, QBS-ar, and PD. Organic farming fields have a greater biological quality of soil, as evaluated by QBS-ar, TR, and PD, indicating improved soil quality/ conditions. In contrast, most of the physico-chemical and fertility parameters are higher in the conventional farming system.