Tomatoes are widely consumed worldwide due to their attractive color, unique flavor, and high levels of antioxidants such as lycopene and carotenoids. However, postharvest tomatoes are highly perishable because of their high moisture content and respiration rate, which accelerate chlorophyll degradation, carotenoid accumulation, softening, and color change during storage. These changes lead to significant economic losses. In this study, the effects of atmospheric cold plasma (ACP) treatment at different intensities (40, 60, and 80 kV) on the storage quality and chlorophyll metabolism of postharvest tomatoes were investigated. Tomatoes were treated with ACP for 5 minutes and stored at 10 ± 0.5 °C for 35 days. Several quality parameters including respiration intensity, firmness, total soluble solids (TSS), titratable acidity (TA), and weight loss rate were evaluated during storage. In addition, the activities of chlorophyll degradation enzymes and the expression of key genes related to chlorophyll metabolism (CLH1, PPH, PAO, and RCCR) were analyzed. The results showed that ACP treatment significantly inhibited respiration intensity and weight loss while maintaining higher firmness, TSS, and TA contents compared with the control group. Furthermore, ACP treatment slowed chlorophyll degradation and carotenoid accumulation, thereby delaying the red ripening process of tomatoes. Among the tested treatments, the 60 kV ACP treatment demonstrated the most effective preservation performance by significantly suppressing chlorophyllase and PAO enzyme activities and downregulating the expression of CLH1, PPH, and RCCR genes. These findings indicate that ACP treatment, particularly at 60 kV, is a promising non-thermal and chemical-free technology for improving the postharvest quality and extending the shelf life of tomatoes.