To enhance the value-added utilization of soybean meal (SBM), this study evaluated the effects of Bacillus subtilis Z1, Bacillus velezensis Z2, and Bacillus amyloliquefaciens Z3 on protein hydrolysis, structural changes, and bioactivity during solid-state fermentation (SSF). Fermentation significantly promoted protein solubilization and hydrolysis, with soluble protein and peptide content increasing by 5.88–6.90-fold and 5.22–6.33-fold, respectively. Notably, free amino acid content increased substantially, particularly essential amino acids (EAAs; 20.26–26.02-fold), with the EAA proportion reaching 47.52% in SBM fermented with B. amyloliquefaciens Z3. SDS-PAGE and HPSEC analysis further demonstrated protein hydrolysis and the alteration in peptide molecular weight distribution after SSF. FTIR analysis revealed that SSF disrupted the native protein conformation and induced pronounced secondary structural rearrangements. Moreover, antioxidant activity and metal-chelating activity of SBM were significantly enhanced after SSF. These findings provide valuable insights into protein bioconversion and support the development of efficient strategies for SBM nutritional upgrading and valorization.