Despite the potential utility of specialized secondary metabolites in a number of commercial applications (pharmaceuticals, consumer and food products, and industrial chemicals), their low abundance in nature presents a significant sourcing and economic obstacle for adoption. Here, we describe the advantages of pairing multivariate modular metabolic engineering of bacteria with systems-level characterization of engineered strains by transcriptomics, proteomics, and metabolomics for expediting the development of economical and sustainable processes for the production of these complex biomolecules.