This work investigated the functional properties, anti-nutritional compounds, functional groups, phytochemicals profile, and antioxidant potential of melon by-products of two different varieties namely T-96 and white ball using standard methods. Melon peels possessed better functional properties while melon seeds showed a lower concentration of anti-nutritional compounds. Fourier transform infrared spectroscopy (FTIR) analysis revealed distinct absorption band properties of functional groups attached to amine, phenol, ketones, and halo compounds, among others. Phytochemical profile (total phenolic and flavonoid content), and antioxidant assay (DPPH, FRAP) were evaluated using different solvent systems (water, methanol, ethanol, and acetone 50% v/v). Ethanol opted as the best solvent for both peel and seed powder and bioactive compounds were quantified by high-performance liquid chromatography (HPLC). Nine different compounds including quercetin, syringic acid, benzoic acid, gallic acid, chlorogenic acid, cinnamic acid, p-coumaric acid, sinapic acid, and caffeic acid were found. Peel extracts presented a higher concentration of bioactive compounds and elevated antioxidant activity as compared to seed extracts. These findings demonstrated that a significant amount of nutrients was present in both parts, particularly the peel. Therefore, it is plausible that by-products derived from melons possess the capacity to serve as a promising reservoir of bioactive chemicals.