Soils contain huge amounts of various living organisms such as worms, fungi and microbes. Those life forms play essential ecosystem services such as filtering water, removing pollutants and providing plant nutrients. However, the effect of soil biodiversity on ecosystem services is still poorly known. Lemanceau et al. show that preservation and valorization of soil biodiversity is a major challenge for agroecology. Their review highlights recent advances in the assessment of soil biological quality. Further research is needed to design decision tools that can be used by farmers to better manage soil biodiversity.