Specificity of monoclonal antibodies (MAbs) is required in diagnostic immunoassays. However, structural homology between a target antigen and other cellular proteins often causes promiscuous cross-reactivity of a MAb to proteins other than its target antigen, thereby hindering specificity. It is proposed in this study that specific proteolytic enzymes could be useful in the reduction or elimination of cross-reactive epitopes while retaining target epitopes for certain MAbs. The hypothesis was tested using a novel ‘S’-type low molecular weight glutenin subunit (LMW-GS-‘S’) and its antibodies. The results demonstrated that the protease, chymotrypsin, markedly reduced the cross-reactivity in samples that would otherwise obscure the specific detection of LMW-GS-‘S’ by MAb F8-14E6 in an enzyme-linked immunosorbent assay (ELISA). Further investigations revealed that the working mechanism for this proteolytic treatment was indeed due to the selective cleavage that destroyed cross-reactive epitopes whilst retaining the intact specific epitope. As more proteases are being discovered or engineered, the successful utilization of protease in immunoassays as reported here will benefit general immunodiagnostic assay development in both medicine and agriculture by targeting specific epitopes with tailored proteolytic treatment of antigens.