Soybean trypsin inhibitor (STI) was used as the sole carbon source, three strains of bacteria capable of degrading soybean trypsin inhibitors were isolated from the interior of soybeans. The 16S rDNA sequence analysis revealed that the strains were Bacillus subtilis LZ013-1, Bacillus pumilus LZ013-2 and Paenibacillus sp. 013-3. Further studies showed that the supernatant of LZ013-2 exhibited a high activity for degrading soybean trypsin inhibitors, and the rate of trypsin inhibitor inhibition was reduced by 73.60% in 2 h. LZ013-1 and LZ013-2 were used in the fermentation of soybean meal, and were s found to degrade trypsin inhibitors efficiently. The trypsin inhibitor activity of the untreated soybean meal was 22.26 mg/g, which was reduced to 0.50 mg/g and 0.63 mg/g, respectively, after liquid fermentation with LZ013-1 and LZ013-2 strains, and decreased to 1.06 mg/g and 1.03 mg/g, respectively, after solid-state fermentation with LZ013-1 and LZ013-2 strains. The proteins with degrading activity were separated from the supernatant of the sample obtained via fermentation with LZ013-2 strain by ammonium sulfate fractionation and gel column chromatography. The separated proteins were identified by mass spectrometry. Two kinds of active proteins were screened and identified as peptidase S8 (Uniprot ID: A0A2T0DB16) and peptidase M84 (Uniprot ID: A8FIH7).