Proteins are complex macromolecules and their three-dimensional structure determines their activity. They play essential roles in soil; they act as reserves of essential nutrients particularly C and N, as enzymes they determine the biogeochemical cycles of essential nutrients, as important components of soil organic matter, they contribute to soil physical stability. After a brief presentation of basic protein chemistry and a description of proteins in soil, including adsorption properties, extraction and characterization, case studies of enzymes, two potentially toxic proteins and a controversial protein known as glomalin-related soil protein are described. A final section presents the pitfalls of soil metaproteomics.