The study aimed at the surface disinfection and shelf life extension of cherry tomatoes using ozone (1O3; 17.2 g/m3 ozone for 4 min and 2O3; 17.2 g/m3 ozone for 12 min), alkaline ionized water (1AEW; pH 10 for 20 min and 2AEW; pH 8.5 for 20 min), and their eight combinations. No significant difference was detected in L*, a*, b*, chroma, hue, and browning index; and titratable acidity, chroma, hue, total antioxidant capacity, and total phenolic and lycopene contents. All the treatments significantly reduced total aerobic mesophilic bacteria, mold and yeast counts and inoculated Salmonella enteritidis, Listeria monocytogenes, and Botrytis cinerea. 1AEW + 2O3 led to a shelf life of 7 weeks, whereas the other treatments and control groups had a shelf life of 5 and 3 weeks, respectively. The joint optimization pointed to 2O3 + 1AEW, 2O3 + 2AEW, and 2AEW + 1O3 as the optimal treatments. Practical applications The fungal and bacterial growths on the tomato surfaces shorten their shelf life. The extension of their shelf life with no adverse effects on their physical, chemical, and bioactive properties with proper disinfection technologies is of great importance. Surface disinfection through the ozone, alkaline ionized water, and their dual combinations extended the shelf life up to 7 weeks without adversely affecting the important quality parameters. The shelf life extension greatly reduces both product and economic losses.