Plants and fungi produce flavonoids, which are valuable secondary metabolites. Flavonoids have several subclasses, including flavones, isoflavones, chalcones, flavanones, anthocyanidins, and flavonols. Apigenin and chrysin belong to the flavone subclass and have benefits for the pharmaceutical, nutraceutical, and cosmetic industries, offering great potential for future applications. Chemical methods for extracting these compounds from plants have several limitations, such as low yield, hazardous materials, poor selectivity, strict conditions, and low effectiveness. To overcome this issue, researchers can introduce novel flavonoid biosynthetic pathways in bacteria and fungi to produce apigenin and chrysin. By using metabolic engineering techniques and synthetic biology, researchers can construct biosynthetic pathways and microbial cell factories in suitable hosts to ensure large-scale production of flavonoids. The hosts used for apigenin production are Escherichia coli, Saccharomyces cerevisiae, and Streptomyces venezuelae, and chrysin can be microbially produced in hosts such as Aspergillus spp., Saccharomyces cerevisiae, Fusarium spp., and Penicillium spp. Enzymes such as C4H, CHI, and CHS catalyze the biosynthesis of apigenin and chrysin. The biosynthesis of apigenin from precursor compounds generates several by-products. A similar biosynthetic pathway produces chrysin from phenylalanine, with cinnamic acid as a by-product. The following book chapter provides a detailed overview of the recent trends and advancements in the microbial production of apigenin and chrysin and the strategies to utilize the metabolic capabilities of microorganisms, such as bacteria and yeast, for the sustainable biosynthesis of these valuable flavonoids. Furthermore, we explore novel engineering techniques that can enhance the production of apigenin and chrysin and their downstream processing for large-scale use.