The effect of melatonin pomegranate tree treatments on fruit quality and bioactive compounds with antioxidant activity at harvest and during storage at 10 °C for 60 days was assayed in two consecutive years, 2019 and 2020. In the first year, trees were treated with 0.1, 0.3 and 0.5 mM of melatonin along the developmental fruit growth cycle, and results showed that bioactive compounds (total phenolics and total and individual anthocyanins) and antioxidant activity at harvest were higher in fruits from melatonin-treated trees than in controls. Other fruit quality parameters, such as firmness, total soluble solids and aril red colour, were also increased as a consequence of melatonin treatment. In fruit from control tress, firmness and acidity levels decreased during storage, while increases occurred on total soluble solids, leading to fruit quality reductions. These changes were delayed, and even maintenance of total acidity was observed, in fruit from melatonin-treated trees with respect to controls, resulting in a fruit shelf-life increase. Moreover, concentration of phenolics and anthocyanins and antioxidant activity were maintained at higher levels in treated than in control fruits during the whole storage period. In general, all the mentioned effects were found at the highest level with the 0.1 mM melatonin dose, and then it was selected for repeating the experiment in the second year and results of the first year were confirmed. Thus, 0.1 mM melatonin treatment could be a useful tool to enhance aril content on bioactive compounds with antioxidant activity and health beneficial effects and to improve quality traits of pomegranate fruit, at harvest and during postharvest storage.