Maintaining the health of soils, and therefore their capacity to carry out the ecosystem functions necessary for sustainable food production, is a complex and evolving area of science. This chapter examines management of mineral fertilisers and organic manures in relation to its effects on soil health in terms of soil organic carbon and nitrogen, soil acidification and soil microbiology. The chapter discusses the optimisation of nitrogen, phosphorus and potassium fertilisers use, together with their interactions and interdependency. The chapter considers agricultural systems and practices and offers suggestions for future areas of research.