Essential oils (EOs), characterized by a promising antimicrobial potential, can ensure the safety and quality of fresh products, encountering the consumer demand for minimally processed foods with clean labels. In this study, oregano and cinnamon EOs, previously characterized for their chemical composition, were first tested in vitro against Staphylococcus aureus DSM 20231^T to assess the Minimum Inhibitory Concentration (MIC) in different conditions. Their effect was evaluated both with culture-dependent (plate counting) and culture-independent (flow cytometry, FCM) methods, considering halved-MIC, MIC, and double-MIC concentrations (125, 250, 500 mg/L), to evaluate the physiological state during EO exposure and the potential cell recovery after EO removal. In the presence of increasing oregano EO concentrations, Staph. aureus cells showed a significant loss of culturability. However, 24h after EO removal, culturability was restored, except for the sample exposed to 500 mg/L. The FCM approach, able to discriminate different cell sub-populations (live, injured, dead), showed that more than 98% of cells were viable after 24h of recovery in samples exposed to 125 mg/L of oregano EO. A high percentage of dead cells (95%) was observed after 30 min of exposure in the presence of 250 mg/L of EO, although after 24h of recovery, an increase in viable cells (up to 30%) was detected. A different behavior was observed with cinnamon EO, which generally exerted a bacteriostatic effect at each concentration. Twenty-four hours after 250 and 500 mg/L cinnamon EO removal /L, dead cells reached a percentage of 53%, while the viable cells ranged from 30% to 9%, respectively. These data highlighted the promise of EO applications in the food industry as an alternative to synthetic additives to obtain safe and natural products. This research was carried out within the framework of the InnoSol4Med project, which is part of the PRIMA program supported by the European Union.