Covering: up to end of June 2018 Baeyer-Villiger monooxygenases (BVMOs) are flavin-dependent enzymes that catalyse the oxidation of ketones and cyclic ketones to esters and lactones, respectively, by using molecular oxygen and NAD(P)H. BVMOs also catalyse sulfoxidations and N-oxidations. BVMOs are widely studied as attractive biocatalysts, but also catalyse key reactions in metabolic pathways of the organisms from which they are sourced. BVMOs are involved in the primary metabolism of atypical carbon sources, thereby conferring an evolutionary advantage to the host organism. In addition, BVMOs catalyse a plethora of diverse Baeyer-Villiger and heteroatom oxidations in the construction of complex secondary metabolites. These natural products often have attractive biological properties, such as anti-bacterial, anti-cancer and anti-proliferative activity, and can have clinical applications. In contrast, BVMOs are also involved in the synthesis of microbial toxins. This review will discuss the inherent roles of type I, type II and type O BVMOs in the metabolism of microorganisms.