Natural products are widely employed in our daily lives as food additives, pharmaceuticals, nutraceuticals, and cosmetic ingredients, among others. However, their supply has often been limited because of low-yield extraction from natural resources such as plants. To overcome this problem, metabolically engineered Escherichia coli has emerged as a cell factory for natural product biosynthesis because of many advantages including the availability of well-established tools and strategies for metabolic engineering and high cell density culture, in addition to its high growth rate. We review state-of-the-art metabolic engineering strategies for enhanced production of natural products in E. coli, together with representative examples. Future challenges and prospects of natural product biosynthesis by engineered E. coli are also discussed. E. coli has emerged as a prominent host for natural product biosynthesis.Improved enzymes with higher activity, altered substrate specificity, and product selectivity can be obtained by structure-based or computer simulation-based protein engineering.Balancing the expression levels of genes or pathway modules is effective in increasing the metabolic flux towards target compounds.System-wide analysis of metabolic networks, omics analysis, adaptive laboratory evolution, and biosensor-based screening can further increase the production of target compounds.Systems metabolic engineering allows the development of engineered E. coli strains that are capable of more efficiently producing diverse natural products.