Soybean products (soyfoods), reported as potential functional foods, are implicated in several health-enhancing properties, such as easing the symptoms of postmenopausal women, reducing the risk of osteoporosis, preventing cardiovascular disease, and antimutagenic effects. Isoflavone, for example, is one of the most important compounds abundantly found in soybean, mainly accounting for the health-enhancing properties as mentioned earlier. However, most biological activities of isoflavones are mainly attributed to their aglycone forms. It has also been demonstrated that isoflavone aglycones are absorbed faster and in greater amount than their glycosides in human intestines. Fortunately, deglycosylation of isoflavones can be achieved during fermentation process by several strains such as lactic acid bacteria, basidiomycetes, filamentous fungus, and Bacillus subtilis with their β-glucosidase activity. This article presents an overview of soybean's chemistry, application, state-of-the-art advances in soybean fermentation processing and products as well as their applications in food and pharmaceutical industries. Different compounds, such as isoflavone, dietary fibers, and proteins which exhibit significant bioactivities, are summarized. The roles of different microorganisms in bioconversion and enhancement of bioactivities of fermented soybean are also discussed.