Fermentation with autochthonous lactic acid bacteria (LAB) has been used as a method of food preservation for thousands of years. In addition to preserving food, fermentation with lactic acid bacteria can improve health-related properties, including nutrient bioavailability and digestibility, of plant foods and dairy foods. This chapter explores the impact of fermentation with LAB on nutrient bioavailability, especially of minerals, and on protein content and digestibility of several different foods. Potential mechanisms and implications for human health are both addressed. The next steps for research and applications of LAB use in functional food development, including low-FODMAP products, low-glycemic index foods, and prebiotic-rich foods, are also addressed.