This study aimed at evaluating an enzymatic strategy to mitigate ochratoxin A (OTA) exposure via contaminated wheat flour. Firstly, the effect of Rhizopus oryzae and Trichoderma reesei, which are both non-toxigenic microorganisms, on OTA, was evaluated. The mycotoxin was degraded by both fungi in the exponential phase of growth. After 48 h, R. oryzae eliminated 63.5% of the mycotoxin whereas, after 72 h, T. reesei reduced it in 57.7%. OTA degradation had high (R > 0.9) and significant (p < 0.05) correlation with OT alpha production and carboxypeptidase A (CPA) activity, an evidence of the fact that CPA-like enzymes were directly related to OTA degradation. To show the applicability of CPA -like enzymes to mitigate OTA exposure, three different CPA sources (animal, vegetable and microbial) were evaluated and applied to contaminated wheat flour. Dough production processes used in bakeries were simulated. All CPAs were able to degrade OTA in flour (from 17 to 78.5%), produce OTa (from 2 to 8.2 ng/g) and reach conversion of 51%. Since the most promising sources were the ones from microbial origin, their use may be a strategy to mitigate the impact of OTA found in wheat flour used in bakeries so as to mitigate the risk of consumer exposure.