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Bell peppers (Capsicum annuum L.) are prone to chilling injury (CI) when stored at temperatures below 7 °C. Melatonin, a natural plant regulator, plays a critical role in defending against different pre- and post-harvest abiotic stresses, including those associated with cold storage. This study aimed to assess the effects of applying exogenous melatonin alone and in combination with a commercial wax on the CI tolerance, postharvest life, and potential biomarker search of red bell peppers. In the initial experiment, the effective melatonin concentration to reduce CI effects was determined. Peppers were sprayed with either distilled water (control) or a melatonin aqueous solution (M100 = 100 μM or M500 = 500 μM) and then stored for 33 d at 4 °C, followed by 2 d at 20 °C. The M500 treatment proved to be more effective in reducing fruit CI incidence (superficial scalds) and metabolic rate, while weight loss, softening, and color were comparable to the control. A second experiment assessed the potential synergistic effects of a combined melatonin and commercial wax treatment on pepper CI and quality. Fruits were sprayed with distilled water (control), melatonin (M500), commercial wax (Wax), or the combined treatment (Wax + M500) and stored for 28 d at 4 °C, followed by 2 d at 20 °C. The Wax + M500 was the most effective in significantly reducing the incidence of fruit CI symptoms and calyx fungal infection. Furthermore, this combined treatment enhanced fruit weight loss prevention compared with individual melatonin or wax treatment. Also, Wax + M500-treated peppers exhibited notable proline accumulation, indicative of a metabolic response counteracting the cold effects, resulting in better fruit stress acclimation. This treatment also preserved the peppers’ color and antioxidant capacity. In summary, these findings highlight the suitability of applying a combined Wax + M500 treatment as a highly effective strategy to enhance the CI tolerance of peppers and extend their postharvest life.