Soils store vast quantities of carbon, more than in the atmosphere or in plant biomass. Decomposition loss of soil carbon is a large term in the global carbon budget and mineralizes nitrogen and other elements needed for plant growth. This chapter develops the biogeochemical foundation and mathematical theory to describe litter decomposition, soil organic matter formation, and nutrient mineralization. The DAYCENT model is used to illustrate the basic details of soil biogeochemical models. Advanced modeling concepts include vertically-resolved soil carbon, microbial models, and competition among multiple nutrient consumers.