This study investigates the impact of melatonin (MT) treatment at varying concentrations (0, 25, 50, 75, 100 µmol L−1) on the post-harvest quality and shelf life of long green pepper fruits stored under low temperature for 28 days. Every 4 days, pepper fruits were examined for the chilling injury (CI) index, weight loss (WL), respiration rates, firmness, electrolyte leakage (EL), reactive oxygen species (ROS), malondialdehyde (MDA) levels, non-enzymatic antioxidant (NEA) content, antioxidant (AO) enzyme activity (superoxide dismutase (SOD), catalase (CAT), and peroxidases (PODs)), and cellular degrading enzymes (polygalacturonase (PG), pectin methylesterase (PME), phospholipase D (PLD), and lipoxygenase (LOX)). MT-treated samples exhibited delayed and reduced CI stress compared to controls, with higher exogenous MT concentrations (>50 µmol L−1) offering significant (p < 0.05) CI reductions. During storage, WL was notably mitigated by MT treatment in the tested samples compared to control samples. This study also demonstrated that MT-treated pepper fruits effectively decelerated respiration rates and consequently preserved pepper firmness. A higher concentration of MT-treated pepper fruits demonstrated a significantly (p < 0.05) lowered level of ROS and MDA while maintaining membrane stability, as evidenced by reduced EL. MT treatment with increasing concentration increased the levels of glutathione (GSH), glutathione disulfide (GSSG), ascorbic acid (AsA), dehydroascorbate (DHA), and total phenolic content (TPC) in the pepper fruits compared to control and thus significantly (p < 0.05) suppressed the ROS production (superoxide anion (O2•−) and hydrogen peroxide (H2O2) radicals) in the pepper fruits. Furthermore, AO enzymes such as SOD, CAT, and POD were also high in the pepper fruits that were treated with higher concentrations of MT (>50 µmol L−1). Additionally, the activities of cellular degrading enzymes (PG, PME, PLD, and LOX), which are linked to senescence and stress-induced physiological disorders, were also effectively regulated by MT-treated (>75 µmol L−1) pepper fruits. Overall, the application of MT at higher concentrations (>75 µmol L−1) demonstrated substantial benefits in preserving the quality and extending the shelf life of pepper fruits during cold storage.