Several isoflavonoids are well known for their ability to act as soybean phytoalexins. However, the overall effects of the soybean–Aspergillus oryzae interaction on metabolism remain largely unknown. The aim of this study is to reveal an overview of nutritive and metabolic changes in germinated and A. oryzae-elicited soybeans. The levels of individual nutrients were measured using the ustulation, ashing, Kjeldahl, and Folch methods. The levels of individual amino acids were measured using high-performance liquid chromatography. Low-molecular-weight compounds were measured through metabolome analysis using liquid chromatography-mass spectrometry. Although the levels of individual nutrients and amino acids were strongly influenced by the germination process, the elicitation process had little effect on the change in the contents of individual nutrients and amino acids. However, after analyzing approximately 700 metabolites using metabolome analysis, we found that the levels of many of the metabolites were strongly influenced by soybean–A. oryzae interactions. In particular, the data indicate that steroid, terpenoid, phenylpropanoid, flavonoid, and fatty acid metabolism were influenced by the elicitation process. Furthermore, we demonstrated that not the germination process but the elicitation process induced daidzein prenylation, suggesting that the soybean–A. oryzae interactions produce various phytoalexins that are valuable for health promotion and/or disease prevention.