The use of reactive oxygen and nitrogen species (RONS) is garnering significant attention as a novel antibacterial strategy to combat the alarming increase of antibiotic resistance. RONS can directly or indirectly inhibit bacterial growth due to their capacity to simultaneously react with extra- and intra- cellular molecules, jeopardizing their biological functions, and engaging in physico-chemical processes that lead to cell death. Multiple studies have been carried out to elucidate their mechanisms of action, and some have been unveiled. However, many others remain elusive, particularly in biologically relevant environments. In this study, we exposed pathogenic bacteria such as Staphylococcus aureus to different ratios of ROS and RNS when naturally produced in combination. To fully investigate their antibacterial effect at molecular level we then carried out RNA sequencing using samples from bacterial cells at their early exponential phase. We observed that bacteria exposed to more RNS than ROS are, metabolically, much more active, triggering biological processes associated with anaerobic respiration, DNA & cell wall/membrane repair, and cell signalling. Although more investigations are needed to further elucidate these specific molecular mechanisms, our study provides new evidence to fully understand why bacteria die or survive under different ROS/RNS ratios.