Microbial production of food bioactive compounds is emerging as a sustainable and high-yield alternative to traditional plant extraction methods. The beneficial health effects of bioactive compounds such as polyphenols, flavonoids, carotenoids (such as lycopene and astaxanthin), alkaloids, polyunsaturated fatty acids (PUFAs), oligosaccharides, and peptides are well known. Using metabolic engineering, synthetic biology, and fermentation technologies, the efficient production of these compounds in microorganisms such as E. coli and S. cerevisiae is now possible with current technologies. These technologies offer higher yields, safety, and cost advantages compared to traditional plant sources. The integration of these methods into food and pharmaceutical formulations demonstrates the industrial potential of microbial biotechnology in the production of health-promoting and functional compounds.