Soy sauce is a liquid condiment made of soybeans and wheat fermented in a brine solution (18%-22 NaCl) called moromi fermentation. Such a high salt concentration may contribute to excessive sodium intake associated with many health problems. However, reducing salt content in moromi could alter the dynamics of the microbial community of moromi, resulting in undesirable changes in the aroma profile. The feasibility of performing low-salt moromi fermentation by introducing starter cultures, such as Tetragenococcus and Zygosaccharomyces species, into moromi has been reported. However, the impacts of their inoculation on the microbial population changes during fermentation remains unknown. This study investigates the effect of Tetragenococcus sp and Zygosaccharomyces rouxii inoculation procedure (ratio, concentration, and inoculation time) on bacterial and fungal population changes during low-salt (6% NaCl) moromi fermentation. Total bacterial and fungal cell counts were obtained by culture on tryptic soy agar (TSA) and potato dextrose agar (PDA), respectively. Adding Z. rouxii twice the amount of Tetragenococcus caused the bacterial population to increase sharply by 3.29 log CFU/mL during the first 8 days of fermentation. Meanwhile, a maximum of 3.70 log CFU/mL increase in yeast counts occurred when Tetragenococcus was added twice the amount of Z. rouxii. Inoculating both cultures simultaneously could maximize yeast population to 7.50 log CFU/mL; however, it suppressed bacterial growth. Simultaneous inoculation could promote bacteria-yeast synergistic growth when 5% inoculum with an equal ratio was used. This study could help soy sauce researchers and manufacturers determine appropriate inoculation procedures to control fermentation better.