Escherichia coli O157:H7 is frequently detected in ready-to-eat produce and causes serious food-borne diseases. The decontamination efficacy of lactic acid (LA) is clearly established. In this study, LA was mixed with acetic acid (AA) to reduce costs while achieving consistent or better inhibitory effects. Time-kill curves and inoculation experiments using fresh-cut spinach and arugula indicated that 0.8%LA+0.2%AA shows similar antibacterial effects to those of 1%LA. To determine whether 1%LA and 0.8%LA+0.2%AA exert antibacterial effects by similar mechanisms, proteomics analysis was used. The proteins related to macromolecule localization, cellular localization, and protein unfolding were uniquely altered after the treatment with 1%LA, and the proteins related to taxis, response to stress, catabolic process, and the regulation of molecular function were uniquely altered after the treatment with 0.8%LA+0.2%AA. Based on these findings, combined with the results of a network clustering analysis, we speculate that cell membrane damage is greater in response to LA than to 0.8%LA+0.2%AA. This prediction was supported by cell membrane permeability experiments (analyses of protein, nucleotide, ATP, and alkaline phosphatase leakage), which showed that LA causes greater membrane damage than 0.8%LA+0.2%AA. These results provide a theoretical basis for the application of an acid mixture to replace LA for produce decontamination.