Traditional fermented foods and beverages have been consumed for thousands of years and are increasingly recognized as functional foods that provide health benefits beyond basic nutrition. They are produced through the metabolic activities of beneficial microorganisms, including Lactobacillus, Bifidobacterium, Saccharomyces, and Leuconostoc, which improve the nutritional quality, safety, and shelf life of foods while promoting human health. Fermentation enhances nutrient bioavailability, synthesizes vitamins and bioactive compounds, degrades anti-nutritional factors, and generates short-chain fatty acids that support gut health and metabolic function. Probiotic microorganisms help maintain intestinal microbial balance, strengthen the gut barrier, inhibit pathogenic microbes, modulate immune responses, and influence the gut–brain axis, thereby contributing to improved digestive, metabolic, cardiovascular, and mental health. Recent advances in microbial fermentation technology have expanded the development of functional foods using indigenous fruits and plant resources, creating sustainable, non-dairy probiotic beverages with enhanced nutritional and therapeutic value. Prebiotics further enhance probiotic survival and activity, while their combination as synbiotics offers synergistic health benefits. Microbial fermentation technology therefore represents an effective and sustainable approach for producing next-generation functional foods that support overall health and disease prevention.