In the fresh produce industry, validation of sanitation efficacy is critical to prevent cross-contamination of produce. The current validation approaches are either based on time-consuming plate counting assays or indirect measurements of chemical properties of wash water. In the study, the focus was to identify biomarkers that can provide direct assessment of oxidative damage in bacteria upon exposure to sanitizers in the presence of fresh produce and correlation of these oxidative biomarkers with logarithmic inactivation of bacteria. Two endogenous bacterial biomarkers, protein carbonylation and thiol oxidation, were evaluated for assessing oxidative damage in Escherichia coli O157:H7 and Listeria innocua during sanitation of pre-cut lettuce leaves with NaOCl or H2O2. Results show that NaOCl treatment was more effective than H2O2 for oxidation of both the intracellular thiols and protein carbonylation in the selected strains. Statistical analysis of the measurements illustrates that oxidation of the intracellular thiol induced by NaOCl or H2O2 was correlated with logarithmic reduction of E. coli O157:H7 and L. innocua. In contrast, changes in the protein carbonylation content were not correlated with reduction in bacterial cell viability. In summary, these results provide a novel approach to validate sanitation efficacy for the fresh produce industry.