In this study the potential targeted use of zinc to inactivate proteinase inhibitors (PI) has been investigated as an alternative to the widely applied heat treatment used industrially for inactivation of PI. Zinc was utilized for the reduction of disulfide bonds leading to the structural changes in proteins, thus affecting the decreased affinity between PI and proteinases. The protein disulfide bond reduction mechanism was studied using a newly developed micellar electrokinetic capillary chromatography (MECC) with the glutathione redox reaction with dithiothreitol (DTT) as model system. This model proved efficient in monitoring the reduction of disulfide bonds in the Kunitz trypsin inhibitor (KTI) and Bowman-Birk inhibitor (BBI). The use of zinc as a reductant resulted in a significant reduction of trypsin inhibitor activity (TIA) of 72% for KTI and 85% for BBI, highlighting zinc as a promising potential agent to reduce the activity of PI as an alternative to heat treatment.