Metabolic changes in fast-fermented bean paste (cheonggukjang) as a function of fermentation time were observed in inoculated Bacillus strains using gas chromatography time-of-flight mass spectrometry (GC-TOF-MS)- and capillary electrophoresis TOF-MS (CE-TOF-MS)-based metabolomics techniques. From the combined GC-MS and CE-MS analysis of fermented cheonggukjang samples, 123 metabolites were recovered (55% by GC-MS and 45% by CE-MS). Multivariate statistical analysis of fermented cheonggukjang samples showed that the separation of metabolites was influenced by the fermentation period (range, 0-72 h) and not by strain. When comparing the metabolites of fermented cheonggukjang with the metabolic pathways, uracil and thymine contents showed a rapid 20-fold increase after 24 h fermentation up to the end of fermentation. Xanthine and adenine levels increased slightly from 24 to 48 h fermentation and then decreased slightly at the end of fermentation. Hypoxanthine and guanine levels also increased remarkably during fermentation. Purine metabolism differed according to the microorganism used for cheonggukjang fermentation. Most intermediates in nucleoside biosynthesis were detected by CE-TOF-MS and were related to amino acid metabolism.