This study addressed the integrated effects of season, slope aspect and land use on faunal population density, diversity and Soil Biological Quality (QBS-ar index) in the mid-hills of the central Nepal Himalaya. It also examined the relationship among these soil quality indicators. Faunal density and QBS-ar were significantly higher during the post-monsoon season when compared with the pre-monsoon season. Faunal population density during both the seasons was higher on the northern rather than southern slope. Faunal density was significantly higher in the forest when compared with agricultural land in both seasons. Soil moisture was positively correlated with soil organic carbon (SOC) and population density, but negatively correlated with soil temperature during the pre-monsoon period. In the post-monsoon season, bulk density was negatively correlated with QBS-ar and population density. Season, slope aspect and land use all had significant effects on the soil quality indicators. This study suggests that high SOC, moisture content and low bulk density lead to increases in population density of soil mesofauna and the QBS-ar index. Therefore, management practices that enhance SOC contents through plant residue retention on farm land, such as farmyard manure application, crop residue mulching and reduced tillage, could increase the numbers and diversity of soil organisms while improving the fertility and productivity of the land.