This dataset contains time-resolved, label-free quantitative proteomic profiles of Staphylococcus aureus ATCC 43300 (MRSA) treated with the natural alkaloid sanguinarine. MRSA cultures were exposed to sanguinarine at the minimum inhibitory concentration (20 mg/L) and sampled at 2, 30, 60, and 120 minutes post-treatment. Untreated samples collected at identical time points served as controls. Proteins were extracted, digested using the FASP method, and analyzed by LC-MS/MS on a Q Exactive HF mass spectrometer. A total of 1,037 proteins were identified across all time points. This dataset supports the findings of a systems-level study exploring the antibacterial mechanism of sanguinarine, highlighting its impact on DNA repair, metabolic stress responses, and suppression of cell division and iron transport. Each condition was performed in three biological replicates.