The aim of this study was to investigate the influence of packaging atmosphere and a thymol dipping solution on the shelf life of caprese salad. Caprese salad was prepared with sliced tomatoes and mozzarella cheese. The samples were pretreated by dipping in a 400-ppm thymol solution and then packaged under air or under a modified atmosphere (65% N2, 30% CO2, and 5% O2). Changes in natural microflora of mozzarella and tomato, the O2 and CO2 in the head space, pH, and sensory characteristics were monitored during storage. The combination of the thymol dip and the modified atmosphere decreased the coliform populations in caprese salad from 5.65 to 4.23 log CFU x g(-1) and extended the shelf life from 3.77 to 12 days. A decrease in the concentration of Pseudomonadaceae from 7.03 to 5.09 log CFU x g(-1) was observed, and the lag phase was prolonged to approximately 3 days. The combination of the modified atmosphere and thymol did not affect the growth kinetics of lactic acid bacteria and enterococci, thus preserving the function of mozzarella cheese in the salad.