BACKGROUNDNatto mucus is mainly composed of poly‐γ‐glutamic acid (γ‐PGA), which affects the sensory quality of natto and has some effective functional activities. The soybean metabolites that cause different γ‐PGA contents in different fermented natto are unclear.RESULTSIn this study, we use untargeted metabolomics to analyse the metabolites of high‐production γ‐PGA natto and low‐production γ‐PGA natto and their fermented substrate soybean. A total of 257 main significantly different metabolites with the same trend among the three comparison groups were screened, of which 114 were downregulated and 143 were upregulated. Through the enrichment of metabolic pathways, the metabolic pathways with significant differences were purine metabolism, nucleotide metabolism, fructose and mannose metabolism, anthocyanin biosynthesis, isoflavonoid biosynthesis, and the pentose phosphate pathway.CONCLUSIONFor 114 downregulated main significantly different metabolites with the same trend among the three comparison groups, Bacillus subtilis (natto) may directly decompose them to synthesize γ‐PGA. Adding downregulated substances before fermentation or cultivating soybean varieties with the goal of high production of such substances has a great effect on the production of γ‐PGA by natto fermentation. The enrichment analysis results showed the main pathways affecting the production of γ‐PGA by Bacillus subtilis (natto) using soybean metabolites, which provides a theoretical basis for the production of γ‐PGA by soybean and promotes the diversification of natto products.This article is protected by copyright. All rights reserved.