In this study, we compared the effects of microwave-assisted extraction (MAE) and ultrasound-assisted extraction (UAE) on the total phenolic content, antioxidant activity, morphological characteristics, and identification of the bioactive compounds in pomegranate seeds. We conducted a phytochemical characterization of the extracts by determining the total phenolic content and total flavonoids. Antioxidant activity was evaluated using ferric reducing antioxidant power (FRAP) and free radical inhibition methods (DPPH and ABTS). Morphological characteristics were analyzed via scanning electron microscopy, UV-Vis and FTIR of the extracts were recorded. Additionally, the main bioactive compounds were identified using HPLC-MS. Our results demonstrated that MAE was the most efficient technique, yielding a higher content of total phenols (35.47 mg GAE/g), total flavonoids (14.44 mg CAE/g) and antioxidant activity (0.19 and 0.41 mmol TEAC/g, as determined by FRAP and ABTS, respectively). In terms of morphological characteristics, UAE induced more changes in the structure of the plant material compared to MAE. According to HPLC-MS analysis, the extract obtained using MAE notably contained coumaric acid, cyanidin, and quercetin, whereas the UAE extract included coumaric acid, cyanidin, kaempferol, and epicatechin. In conclusion, this study demonstrated that MAE is a more efficient method than UAE for extracting bioactive compounds. Pomegranate seeds may represent a potential source of these compounds for application in various industrial areas.