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Until now, <i>Streptoverticillium mobaraense</i> transglutaminase (TG) is the only commercialized TG, but limited information is known about its selection tendency on crosslinking sites at the protein level, restricting its application in the food industry. Here, four recombinant <i>Bacillus</i> TGs were stable in a broad range of pH (5.0–9.0) and temperatures (<50 °C), exhibiting their maximum activity at 50–60 °C and pH 6.0–7.0. Among them, TG of <i>B. cereus</i> (BCETG) demonstrated the maximal specific activity of 177 U/mg. A structural analysis indicated that the Ala147-Ala156 region in the substrate tunnel of BCETG played a vital role in catalytic activity. Furthermore, bovine serum albumin, as well as nearly all protein ingredients in soy protein isolate and whey protein, could be cross-linked by BCETG, and the internal crosslinking paths of three protein substrates were elucidated. This study demonstrated <i>Bacillus</i> TGs are a candidate for protein crosslinking and provided their crosslinking mechanism at the protein level for applications in food processing.