Changes in dough metabolite profiles during fermentation can provide insight into the relationship with bread quality. We examined the changes in dough ingredients according to the amount of yeast and with or without punching. Metabolomic analysis of dough during fermentation utilized proton nuclear magnetic resonance (¹H NMR) spectroscopy and gas chromatography/mass spectrometry (GC/MS) techniques. There were small differences in the water-soluble compounds of the dough between with and without punching, but differences in the volatile compounds were found. Doubling the amount of baker's yeast halved the fermentation time, but the contents of some metabolites were different. Correlation analysis indicated that some metabolites showed moderately strong correlations with the specific volume of baked bread. Overall, this study provides insights into the extensive metabolomic diversity associated with yeast activity.