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Background: Soy sauce is applied as a seasoning in daily life in East Asia. High amounts of salt in soy sauce can inhibit microbial growth in its production and preservation. However, the elevated salt content in food might increase the health risk. Low salt fermentation is rarely used in soil sauce production because of the potential harmful lactic acid bacteria growth. Therefore, dilution after high salt fermentation is commonly used to reduce the salt concentration. Methods: This study aims to treat the low salt fermented soy sauce with a high hydrostatic pressure process (HPP) to eliminate the harmful bacteria and to analyze the microbial community change compared with that in traditional high salt fermentation. Results: The results showed that the bacterial diversity was increased in low-salt and high-pressure (LS-HP)-treated soy sauce, though the bacterial abundance was decreased. Relative abundance in high-salt (HS), low-salt (LS), and LS-HP-treated soy sauce showed specific bacterial strains in the LS-HP group. Similarly, the fungal diversity was also increased in LS-HP-fermented soy sauce and the detected OTUs were increased. The fungi sensitive to salinity and pressure were indicated in our results. Conclusions: The present study suggests the enhanced bacterial and fungal diversity and different microbial community in HS, LS, and LS-HP-treated soy sauce, as well as the availability of LS and HPP treatment on soy sauce production.