Phenolics are a class of plant-derived natural secondary metabolites with good anticancer, anti-inflammatory, antimicrobial and antioxidant activities. In addition to being natural health-benefit compounds abundant in food, phenolic compounds may also have the potential to be ideal food additives and preservatives. Unlike the traditional plant extraction and chemical biosynthesis methods, metabolic engineering of microbes provides a possible way to sustainably produce phenolic compounds on a large scale, with high commercial availability and low environmental impact. In the last decade, many phenolic compounds have been successfully synthesized and optimized in the model organisms, especially in Escherichia coli and Saccharomyces cerevisiae. In this review, the recent efforts on their sustainable biosynthesis of phenolic compounds for functional food applications are systematically introduced and discussed.