Complex relationships exist between different components of organic agriculture and the quantity and quality of the end products depend on the functioning of the whole system. As such, it is very difficult to isolate soil fertility from production and environmental aspects of the system.
Crop rotation is the central tool that integrates the maintenance and development of soil fertility with different aspects of crop and livestock production in organic systems. Organic nutrient supply to crops depends on the use of legumes to add nitrogen to the system and limited inputs of supplementary nutrients, added in acceptable forms. Manures and crop residues are carefully managed to recycle nutrients around the farm. Management of soil organic matter, ensure good soil structure and biological activity, important for nutrient supply, health and productivity of organic crops. Carefully planned diverse rotations help reduce the incidence of pests and diseases .