Microbial fermentation has been a warhorse of food manufacturers since ancient times. Historical products such as bread, yogurt, beer, and wine are made using microbes selectively isolated because their metabolites confer unique taste and special nutritional features to these and other fermented products. Recently, these metabolites have been included in food formulations to improve both organoleptic and nutritional properties of a wide range of food products. However, the production yield of these dietary compounds is often lower than expected. In this chapter, we describe how microbial fermentation can be used as a suitable approach to improve the nutritional and sensory quality of food and pay special attention to the use of agroindustrial waste as an inexpensive substrate for the synthesis of dietary compounds. Furthermore, we review some promising reports on the use of genetic engineering of microbes to improve their performance in terms of production yield. In addition, we mention some bacterial species that can reduce the level of residual nitrites, a well-known group of carcinogenic compounds, in meat products.