Currently, there is a need for new technological interventions to guarantee the microbiological safety of ready-to-eat (RTE) foods. Non-thermal atmospheric plasma (NTAP) has emerged as a promising strategy for inactivating microorganisms on thermo-sensitive foods, and the elucidation of its mechanisms of action will aid the rational optimization and industrial implementation of this technology for potential applications in the food industry. In this study, the effectiveness of NTAP for inactivating strains of Salmonella Enteritidis, Salmonella Typhimurium, Escherichia coli O157:H7 and Listeria monocytogenes contaminating the surface of different sliced RTE foods (“chorizo”, salami, bacon, smoked salmon, tofu and apple) was investigated. In addition, to further assess the bacterial inactivation mechanisms of NTAP, the morphological and physico-chemical damages in bacterial cells were analyzed. NTAP was effective for the surface decontamination of all products tested and, especially, of cut apple, where the microbial populations were reduced between 1.3 and 1.8 log units for the two Salmonella strains and E. coli O157: H7, respectively, after 15 min of exposure. In the rest of foods, no significant differences in the lethality obtained for the E. coli O157:H7 strain were observed, with inactivation rates of between 0.6 and 0.9 log cycles after a 15-min treatment. On the other hand, the strains from the rest of pathogenic microorganisms studied were extremely resistant on tofu, where barely 0.2–0.5 log units of inactivation were achieved after 15 min of plasma exposure. S. Enteritidis cells treated for 10 min exhibited noticeable morphological and structural changes, as observed by transmission electron microscopy, which were accompanied by a loss in membrane integrity, with an increased leakage of intracellular components and uptake of propidium iodide and marked changes in regions of their FTIR spectra indicating major alterations of the cell wall components. Overall, this indicates that loss of viability was likely caused for this microorganism by a significant damage in the cellular envelopes. However, the plasma-treated cells of L. monocytogenes did not show such obvious changes in morphology, and exhibited less marked effects on the integrity of their cytoplasmic membrane, what suggests that the death of this pathogenic microorganism upon NTAP exposure is more likely to occur as a consequence of damages in other cellular targets.