Doenjang is a traditional Korean fermented soybean-based food that is now produced industrially as traditional Doenjang and modernized Doenjang, depending on the conditions of the manufacturing process. In this study, the effect of the production process on Doenjang metabolites was analyzed using untargeted capillary electrophoresis time-of-flight mass spectrometry (CE-TOF/MS). Of the 247 metabolites detected in 19 traditional and three modernized Doenjang samples, the level of 55 metabolites were significantly different between the two production groups. The S-plot of the orthogonal projection to latent structures-discriminant analysis (OPLS-DA) revealed that nine compounds (tryptamine, 2-phenylethylamine, citrulline, gamma-aminobutyric acid, putrescine, tyramine, 2-aminoisobutyric acid, stachydrine, and N⁵-ethylglutamine) were highly distributed in the traditional group, and six compounds (arginine, citric acid, choline, cytidine, hypoxanthine, and glucaric acid) were considered distinguishable metabolites of the modernized group. Microbial community analysis indicated that the levels of these metabolites were significantly altered by the presence of Bacillus spp., Enterococcus faecium, Tetragenococcus halophilus, Aspergillus oryzae, Penicillium spp., and Saccharomyces cerevisiae. These findings better our understanding of the influence of the manufacturing process on Doenjang production in terms of both microbial activity and metabolite profiles.