This study investigated the effect of enzymatic treatment on the allergenicity of α‐lactalbumin (ALA). Utilising the BIOPEP database, we identified five proteases that optimally clear allergen epitopes, while considering cost‐efficiency. Notably, alkaline protease demonstrated the highest antigen reduction rate of 46.46%, with a hydrolysis degree of 30.01%, and 87.80% of the resulting peptides were found to be smaller than 1 kDa. Peptidomics analysis revealed AA32–38 and AA42–48 as key linear epitopes of ALA. Furthermore, alkaline protease treatment significantly reduced the proportion of hydrophilic amino acids, thereby decreasing the allergen potential of ALA by lowering its IgE/IgG binding affinity.