Wheat gluten elicits a pro-inflammatory immune response in patients with celiac disease. The only effective therapy for this disease is a life-long gluten-free diet. Gluten detoxification using glutenases is an alternative approach. A key step is to identify useful glutenases or glutenase-producing organisms. This study investigated the gluten-degrading activity of three Bacillus cereus strains using gluten, gliadin, and highly immunotoxic 33- and 13-mer gliadin peptides. The strain AFA01 was grown on four culture media for obtaining the optimum gluten degradation. Complete genome sequencing was performed to predict genes of enzymes with potential glutenase activity. The results showed that the three B. cereus strains can hydrolyze gluten, immunotoxic peptides, and gliadin even at pH 2.0. AFA01 was the most effective strain in degrading the 33-mer peptide into fractions containing less than nine amino acid residues, the minimum peptide to induce celiac responses. Moreover, growth on starch casein broth promoted AFA01 to degrade immunotoxic peptides. PepP, PepX, and PepI may be responsible for the hydrolysis of immunotoxic peptides. On the basis of the potential of gluten degradation, AFA01 or its derived enzymes may be the best option for further research regarding the elimination of gluten toxicity.