The detection of cytoplasmic metabolites that differentiate between control and treatment samples may help in controlling S. aureus adaptation and survival. Indeed, the outcomes of this study indicated that the incubation of S. aureus with both cold and osmotic treatments led to significant variations in the cytoplasmic metabolite composition. Exposing the bacteria to lower temperature of 4°C resulted in a significant reduction in the majority of analyzed metabolites, whereas the cells incubated with elevated NaCl conditions had increased levels of identified metabolites. It is evident that certain strategies were developed to ensure survival during the incubation in low temperature and elevated NaCl to obtain optimal metabolism status by altering metabolite levels. It was thus concluded that these adjustments in metabolite levels may have assisted this bacterium to survive alterations in environmental conditions. More knowledge of adaptability and survival capability of S. aureus under various stress conditions may lead to a better understanding of sterilization methods and food storage as well as control of infection.