In recent years, advances in theoretical methods and computational capabilities have made it possible to investigate reaction mechanisms in enzymes. Density functional theory (DFT) is commonly used to study reactions in model systems, while combined quantum mechanical/molecular mechanical (QM/MM) approaches allow the treatment of the complete solvated enzyme and thus provide insight into the mechanistic influence of the protein environment. This review starts with a brief overview over the available DFT and QM/MM methodology and then summarizes recent theoretical studies on biocatalysis by molybdenum-containing enzymes. It focuses on the reactions in members of the dimethylsulfoxide reductase, sulfite oxidase, and xanthine oxidase families, with special emphasis on the QM/MM studies of the latter. It concludes with a brief survey of theoretical work on some other molybdenum- and tungsten-containing enzymes.