To compare γ-glutamyl di- and tripeptides generated by different Bacillus strains and investigate the impact of substrates on the production of γ-glutamyl peptides, six strains of four species, including B. subtilis, B. velezensis, B. amyloliquefaciens and B. paralicheniformis, were cultivated in a standard brain heart infusion (BHI) broth and a medium consisting of hemoglobin hydrolysates (HH) for six days. Quantitative analysis of free amino acids and γ-glutamyl peptides, as well as determination of bacterial growth and γ-glutamyltransferase activity were carried out. Results revealed that all Bacillus strains could generate a series of γ-glutamyl dipeptides in both media. Most strains produced higher concentrations of target peptides in the HH medium (up to 83.56 μM), which correlated with higher levels of free amino acids in the medium. Glutathione was detected only in the BHI medium with B. subtilis PRO84, B. velezensis PRO76, B. altitudinis PRO107, and B. paralicheniformis PRO109 (up to 0.61 μM), indicating the glutathione-forming ability of these Bacillus strains. Production of γ-glutamyl peptides was influenced by both the choice of strain and growth medium, with the medium exerting a more pronounced impact than the strain. This study highlights the importance of selecting the appropriate substrate and Bacillus strains to produce desired γ-glutamyl peptides as enhancers of koku, potentially inspiring the conversion of meat side streams into valuable kokumi seasonings.