Soy sauce is an increasingly popular oriental fermented condiment produced through a two-step fermentation process called koji (solid-state fermentation) and moromi (brine fermentation). Complex microbial interactions play an essential role in its flavor development during the fermentation. Tetragenococcus halophilus and Zygosaccharomyces rouxii are predominant among the microbes involved in the moromi stage. Despite their importance for producing a wide range of volatile compounds, antagonism can occur due to different growth condition requirements. Furthermore, microbial interactions in moromi fermentation are affected by current efforts to reduce salt in soy sauce, in order to tackle slow fermentation due to low metabolic activity of microbes and increased health risk related to high sodium intake. Attempts to enhance and accelerate flavor formation in the presence of high salt concentration include the inoculation with mixed starter cultures, genetic modification, cell, and enzyme immobilization. Although salt reduction can accelerate the microbial growth, the flavor quality of soy sauce is compromised. Several approaches have been applied to compensate such loss in quality, including the use of salt substitutes, combination of indigenous cultures, pretreatment of raw material and starter cultures encapsulation. This review discusses the role of microorganisms in soy sauce production in relation to flavor formation and changes in production practices.