Phosphorus is a key element for life that occurs in living cells as a structural part of many key biochemicals. Phosphorus plays important functional roles in biocatalysis, such as making metabolic reaction steps irreversible by transferring energy-rich groups, using phosphate groups as leaving groups, or selectively hydrolyzing phosphorus–oxygen or phosphorus–nitrogen bonds. The large number of biocatalysts known to catalyze the transfer of phosphorus-containing groups from donor molecules to acceptor molecules covers a wide variety of reaction classes. Bioprocessing technology can and should replicate these naturally occurring reactions. We illuminate some strategic advantages of this promising technology for developing biocatalytic processes and separation steps. Constraints, opportunities, and outlooks for implementing green engineering procedures to establish sustainable production processes are discussed.