Soy whey wastewater generated from tofu production contains rich nutrients but has a very short shelf‐life. In this study, salt‐added soy whey was used as the liquid substrate instead of brine for the production of soy whey soy sauce (SWSS), and the sensory description, physicochemical properties, microbial community and volatile compounds were compared with traditional soy sauce (SS). The results indicated that amino nitrogen and reducing sugar were significantly higher in SWSS at the initial fermentation, but physicochemical properties and intensities of sensory attributes were not significantly different in the final product of SWSS and SS. Meyerozyma was the predominant genus at 90 and 120 days, while Candida became the most abundant at the end of fermentation in SWSS. A total of 89 volatile compounds were identified in SWSS and SS, correlation analysis indicated the acetic acid and phenylethyl alcohol were negatively affected by Aspergillus while positively affected by Candida. This study provided a promising and zero‐waste solution to biotransforming soy whey into soy sauce.