The effect of solid-state fermentation by Rhizopus oligosporus RT-3 on the nutritional and functional properties of soybean meal (SBM), wheat germ (WG), and their mixtures (2SBM-1WG, 1SBM-1WG, and 1SBM-2WG) was investigated. During fermentation, the contents of protease, α-galactosidase activity, soluble protein, peptide ( < 10 kDa), glucose, galactose, antioxidants, phenolic acids, and aglycones isoflavones increased in all samples. In contrast, anti-nutritional factors such as stachyose, raffinose, trypsin inhibitor activity, and glucoside isoflavones decreased significantly. The volatile compound analysis identified 53 compounds, including 12 alcohols, 7 aldehydes, 4 esters, 6 ketones, 15 acids, and 9 other compounds in the fermented and non-fermented samples, the addition of wheat germ improved the taste and flavor by increasing the ester content, especially ethyl decanoate, ethyl octanoate, and hexamethyl methyl, Meanwhile, fermentation decreased the 1-hexanol level from soybean meal. The fermented 1SBM-1WG blend showed the most favorable flavor and a well-balanced nutritional value. Metabolic profiling of fermented (1SBM-1WG) and non-fermented (NF-1SBM-1WG) samples revealed 1506 metabolic peaks. Among these, 20 differential metabolites were significantly affected by fermentation (P-value < 0.05; VIP = 1.165). This comprehensive analysis reveals that the 1SBM-1WG ratio represents the optimal substrate formulation for fermentation, providing a balanced nutritional profile and improved functional properties.