Banana pericarp is highly susceptible to chilling injury (CI), negatively affecting its quality and shelf life. Melatonin (MT), a plant tryptophan derivative, has shown promising effects in mitigating CI and related physiological disorders in tropical and subtropical fruits. This study investigated the efficacy of MT at different concentrations (0, 50, and 100 µM/L) in the coating of banana pericarp to control CI and physicochemical degradation during storage at 7 °C for five days, and on each day, fruits were assessed for quality. The MT100 treatment significantly (p < 0.05) mitigated the severity of the CI index, electrolytic leakage (EL), and malondialdehyde (MDA) levels. Reactive oxygen species (ROS) levels were substantially higher in control samples, whereas MT treatments notably suppressed their increase. Glutathione (GSH) and ascorbic acid (AA) levels were elevated in those banana pericarps treated with higher MT concentrations. Although total phenolic content (TPC) and total carotenoid contents (TCC) were increased in MT-treated samples, the MT concentrations did not significantly affect them. The level of phenolic compounds, such as gallic acid (GA), chlorogenic acid (CA), quinic acid (QA), protocatechuic acid (PA), and catechin (CC), exhibited continuous growth during the storage period, with the highest levels found in MT100-treated samples. Activities of enzymes such as lipoxygenase (LOX), phospholipase D (PLD), phenylalanine ammonia-lyase (PAL), and polyphenol oxidase (PPO) were significantly (p < 0.05) higher in control samples and rose continuously over time, yet were effectively reduced in MT-treated pericarps. This study shows that applying a higher MT coating (100 µM/L) to bananas is an effective post-harvest strategy to considerably lower the incidence of CI and associated losses.