Soy sauce is considered the most important food condiment in China for its distinct fragrance and salty taste. Highly valued for its unique tastes and flavours, soy sauce exhibits many beneficial functions, such as 4-hydroxy-2(or 5)-ethyl-5(or 2)-methyl-3(2H)-furanone and 4-ethylguaiacol. Soy sauce has been widely used in Asian countries for cooking. With the rapidly growing popularity of these unique tastes and flavours, it is important to have a comprehensive reference of its functional benefits. Meanwhile, the genes encoding the major enzymes of metabolism exhibit specialised roles. This review provides a valuable source for the abundant metabolism genes of strains and current knowledge on antioxidant activity, antihypertensive effect, anticarcinogenic activity, fortification and their relationships with soy sauce tastes and flavours.