The small molecule domain of biological cellular systems is closely related to the synthesis and breakdown of larger molecules such as DNA, RNA, proteins, or polysaccharides. Although the analysis, identification, characterization and synthesis of metabolites has a long history of milestone discoveries, it continues to be of great interest in the search for novel biological activities, metabolic pathways, diagnostic and therapeutic applications. Biologically active metabolites benefit from advantages in diffusion and transport for various interactions with proteins and nucleic acids and regulatory events. Therefore, metabolism is receiving renewed interest and meets molecular biology in the context of a true molecular understanding of cellular systems in health and disease. The analysis of the spatial and temporal organization of biocatalysis in cellular and subcellular systems provides valuable clues for resource- and energy-efficient synthetic routes to natural metabolites. At the same time metabolites are needed for these analyses and the synthesis of metabolites is experiencing a renaissance. A Systems Biocatalysis approach to the synthesis of metabolites aims at biocatalytic route designs with high molecular economy. Biocatalytic reaction platforms have been successfully developed as preferred synthetic methodology for a number of reaction classes, which can be assembled in the selection of routes to metabolites.