Soy sauces can be classified into three categories based on the production method used: honjozo, kongojozo (mixed-brewing, amino acid-decomposed), and kongo (mixed, amino acid-decomposed) soy sauces. Although differences in flavor between traditional (honjozo) and modern (amino acid-decomposed) soy sauces are clear, knowledge of the differences in compound profiles and the relationship between these and the sensory characteristics that affect soy sauce quality is limited. Therefore, this study aimed to investigate the differences between traditional and modern soy sauce compounds using metabolomic analysis, and to investigate the compounds that may be correlated with differences in flavor. Non-targeted gas chromatography/mass spectrometry (GC/MS) metabolomics analysis was performed on nine traditional and six modern soy sauces to annotate 239 soy sauce compounds. Principal component analysis suggested that the production methods used formed clusters that affected the types and amounts of soy sauce compounds, and that the production method had a greater effect on soy sauce composition than did the aging barrels or type of soybean used. Traditional soy sauce was characterized by alcohols and esters, whereas modern soy sauce was characterized by pyrazines. A sensory evaluation revealed that traditional soy sauce was characterized by bitterness and astringency, whereas modern soy sauce was characterized by sweetness and viscosity, suggesting that the method of soy sauce production influences flavor differences. This is the first study to comprehensively characterize the effects of production methods, aging barrels, and soybean types on soy sauce compounds and how these compounds contribute to differences in flavor.