Microbial fermentation represents a transformative biotechnological process that significantly enhances the nutritional quality of agricultural produce. This comprehensive review examines the mechanisms by which fermentation improves bioavailability, increases nutrient content, reduces antinutrients, and generates bioactive compounds in plant and animal-derived foods. We analyze traditional fermentation practices alongside modern biotechnological approaches, highlighting their roles in addressing global malnutrition and food security challenges. The integration of controlled fermentation processes offers sustainable solutions for improving dietary quality while preserving food resources and extending shelf life.