Soybean processing, e.g., by soaking, heating, and fermentation, typically results in diverse metabolic changes. Herein, multivariate analysis-based metabolic profiling was employed to investigate the effects of fermentation by Aspergillus oryzae or Bacillus subtilis on soybean substrates extracted at 4, 25, or 55 °C. As metabolic changes for both A. oryzae and B. subtilis were most pronounced for substrates extracted at 55 °C, this temperature was selected to compare the two microbial fermentation strategies, which were shown to be markedly different. Specifically, fermentation by A. oryzae increased the levels of most organic acids, γ-aminobutyric acid, and glutamine, which were ascribed to carbohydrate metabolism and conversion of glutamic acid into GABA and glutamine. In contrast, fermentation by B. subtilis increased the levels of most amino acids and isoflavones, which indicated the high activity of proteases and β-glucosidase. Overall, the obtained results were concluded to be useful for the optimization of processing steps in terms of nutritional preferences.