The Green Revolution boosted agricultural production approximately 2.5 times and was associated with an approximately 40% price reduction in the cost of food (MA, 2005). Following on the euphoria of this success there has been increasing pressure to diversify production and to improve the planet’s environment (Hubert et al., 2010). Successful realization of this pressure will require better soil management. However, current conditions are very different from what they were 50 years ago. The success of the Green Revolution came at the expense of the natural capital, such that 18 of the 24 currently acknowledged ecosystem services have been impaired. Although soils have aided climate regulation by sequestering an estimated 2 Gt carbon (C) per annum from fossil fuel burning, they have lost part of their capacity to regulate hydrological fluxes and nutrient cycles and therefore to support plant production. The soils of the earth are now being asked to produce 70% more food over the next 35 years, while also producing biofuels, regulating climate through further C sequestration, and helping to conserve biodiversity. However, the other side of this coin is the declining amount of land remaining available for conversion to agroecosystems and the increased cost of energy, which has led to a substantial increase in the price of fertilizers. Further, world sources of phosphorus (P) are being rapidly depleted and the toxic effects of pesticides are now forcing the replacement of these former pillars of intensive agriculture with new technical options. Agriculture now needs to sustain high levels of production while preserving or restoring the natural capital of the soil. Maintenance of an appropriate level of soil biodiversity is critical to achieving this goal, but in order to protect the soil resource and optimize its long-term use, new land use practices are needed to be developed, based on much greater understanding of the factors controlling its functioning. This article summarizes the current knowledge of the composition and taxonomic richness of the soil biota. It then examines the participation of the soil biota in the major soil functions and discusses ways to reconcile the conservation and/or improvement of this natural capital with the production of critical ecosystem goods and services.