Soil health is dependent upon complex bio-physical and bio-chemical processes which interact in space and time. Microrganisms and fauna in soil comprise highly diverse and dynamic communities that contribute, over either short or long time frames, to the transformation of geological minerals and release of essential nutrients for plant growth. Certified organic soil management practices generally restrict the use of chemically-processed highly soluble plant nutrients, leading to dependence on nutrient sources that require microbial transformation of poorly soluble geological minerals. Consequently, slow release of nutrients controls their rate of uptake by plants and associated plant physiological processes. Microbial and faunal interactions influence soil structure at various scales, within and between crystalline mineral grains, creating complex soil pore networks that further influence soil function, including the nutrient release and uptake by roots. The incorporation of organic matter into soil, as either manure or compost in organic farming systems is controlled to avoid excessive release of soluble nutrients such as nitrogen and phosphorus, while simultaneously contributing an essential source of carbon for growth and activity of soil organisms. The interdependence of many soil physical and chemical processes contributing to soil health is strongly linked to activities of the organisms living in soil as well as to root structure and function. Capitalizing on these contributions to soil health cannot be achieved without holistic, multiscale approaches to nutrient management, an understanding of interactions between carbon pools, mineral complexes and soil mineralogy, and detailed examination of farm nutrient budgets.