In this work, we investigated the structural and biological properties of soybean protein isolate (SPI) after 0–8 h hydrolyzation with cell envelope proteinase (CEP) extracted from Lactobacillus delbrueckii subsp. bulgaricus. CEP hydrolysis increased the β-sheet and red-shifted the fluorescence peak, while decreasing the α-helix, indicating the unfolding of soybean proteins. Increased surface hydrophobicity and fluorescence of the soybean protein hydrolysates were correlated with the increased hydrophobic amino acid (from 209.67 to 217.6 mg/100 g). CEP tended to hydrolyze the N- and C-terminal regions of sequences dominated by Gly and Leu, which enhanced the antioxidant activity of the SPHs (lowest IC50s value of ABTS•+ and hydroxyl radical scavenging activity were 0.324 ± 0.006 mg/mL and 0.365 ± 0.001 mg/mL after 4 h hydrolysis). Comparison with the database of bioactive peptides suggested various potential biological activities, including antioxidant activity, angiotensin-converting enzyme inhibitory activity and dipeptidyl peptidase-IV inhibitory activity. The study findings have theoretical significance for the development of CEP hydrolysis and novel bioactive soybean peptides.