Staphylococcus aureus is an opportunistic pathogen responsible for a significant proportion of nosocomial infections, largely due to its remarkable ability to adapt to diverse and dynamic environmental conditions, such as those found on human skin and within wound sites. This study investigated the bacterium’s physiological responses to environmental variables including pH (6–8), temperature (35–37°C), and salinity (0–5% NaCl). Comprehensive proteomic analyses revealed significant alterations of cytoplasmic and secreted proteins. Sixty differentially regulated cytoplasmic proteins were identified and categorized into ten functional groups including protein biosynthesis, metabolism, signal transduction, and energy generation. Principal component analysis (PCA) demonstrated distinct amino acid and protein expression profiles corresponding to specific environmental conditions. Notably, elevated salinity at pH 6 led to a general downregulation of cytoplasmic and ribosomal proteins, whereas at pH 8, protein levels increased. However, ribosomal proteins L32 and S19 remained stable across all tested conditions. Secreted protein analysis further indicated substantial shifts in both abundance and distribution in response to stress conditions. These findings support the hypothesis that S. aureus actively remodels its proteome and metabolic processes to maintain homeostasis and ensure survival under physiologically relevant stress conditions.