Maintaining the health and fertility of our soils is central to the productivity of farming systems because of the key role that both health and fertility play in crop production. The links between soil health and the health consumers (both animal and human) and the wider ecosystem are important underlying themes of organic agriculture. Organic farming relies primarily on the use of crop rotations together with manures and crop residues produced on farm and limited allowable off-farm inputs to maintain soil fertility and health. Organic farming requires a long-term perspective on how crop rotations and organic inputs can be used to provide nutrients in synchrony, with crop demand allowing crop nutrition to be optimised while nutrient losses are minimised. Our understanding of the form and function of soil biota has increased rapidly in recent years, but the practical application of this knowledge remains a major challenge.