Amaranthus tricolor has been reported to contain some antimicrobial compounds, such as alkaloids, polyphenols, and terpenoids. However, its effect on Staphylococcus aureus has been less well researched. Therefore, this study was designed to evaluate the antimicrobial activity and possible mechanism of action of the Amaranthus tricolor crude extract (ATCE) against S. aureus and potential application in cooked meat. The antimicrobial activity against S. aureus was assessed by disk diffusion, minimum inhibitory concentration (MIC) determinations, and growth curve. The changes of bacterial membrane potential, intracellular pH (pHin), content of bacterial protein and DNA, and cell morphology were measured to indicate its antimicrobial mechanism of action. The effects of different concentrations of ATCE on bacterial counts, pH, and color of lean cooked pork during 6 d storage were assessed. The results showed that the diameter of inhibition zone (DIZ) and MIC of ATCE against S. aureus were 12.63 ± 0.34 to 12.94 ± 0.43 mm and 80 mg/mL, respectively. The mechanism of action of ATCE against S. aureus was associated with cell membrane depolarization, reduction of pHin, decrease of bacterial protein content, cleavage of cell DNA, and leakage of cytoplasm. Besides, ATCE resulted in a reduction of 1.02 log CFU/g from 3 log CFU/g in S. aureus-inoculated lean cooked pork. The pH values of lean cooked pork treated with ATCE did not show significant changes as the storage time increased, but there was a slight and significant decrease seen with the application of 1 and 2 MIC of ATCE. After treating with ATCE, the color of lean cooked pork showed less lightness (L*), more redness (aâ), similar yellowness (b*), stronger chroma (C*), and weaker hue angle (h*) during 6 days of storage. Therefore, these findings indicate that ATCE has antimicrobial activities against S. aureus and possesses latent energy to become a natural preservative to maintain the quality of lean cooked pork.