The present invention provides a method for reducing EC precursor, citrulline, in soy sauce by inoculating T. halophilus BBE R23 during soy sauce fermentation. Compared to the control, citrulline and EC in soy sauce prepared with T. halophilus BBE R23 is decreased by 86% and 50%, respectively. Addition of 106 CFU/mL T. halophilus BBE R23 also increases volatile flavoring compounds and free fatty acids concentration in the soy sauce product. The present invention provides a method of making soy sauce that not only reduces accumulation of EC precursor citrulline but also improves soy sauce flavor.