Animal manure is the most important source of nutrients applied in most organic farming systems. Nitrogen (N) is often the most yield-limiting factor in non-leguminous crops, and thus lack of N may cause reduced yield and low protein content in many crops. In addition, N is the nutrient that is most easily lost, and these losses may have serious environmental impacts. This chapter reviews literature related to manure management and nutrient utilization, including ways to improve manure management in animal housing, during storage and after application in the field. The chapter considers anaerobic vs aerobic manure storage (composting), manure application methods and their effects on N utilization and soil carbon storage. The chapter explains how phosphorus and potassium applied in manure contribute to crop nutrient supply, especially when the soil availability is low, and also contribute to maintaining the soil fertility. Finally, the chapter looks ahead to future research trends in this area and provides detailed guidance on further reading on the subject.