Soil biodiversity vastly exceeds aboveground biodiversity, and is prerequisite for ecosystem stability and services. This review presents recent findings in soil biodiversity research focused on interrelations with agricultural soil management. Richness and community structure of soil biota depend on plant biodiversity and vice versa. Soil biota govern nutrient cycling and storage, soil organic matter (SOM) formation and turnover. Agriculture manipulates plants, soils and SOM. With intensification, regulation of functions through biodiversity is replaced by regulation through agricultural measures. Fertilizers and agrochemicals exert strong effects on soil biodiversity and functioning. Resulting community shifts feed back on soil functions such as carbon and nutrient cycling and pest control. Therefore, agricultural systems with less inputs may promote self-regulating systems and higher biodiversity.