Agricultural byproducts such as fruit peels represent an underutilised source of high value bioactive compounds. The present study investigates the comprehensive volatile and non-volatile metabolomic profiling of four distinct fruit cultivars - pineapple, banana, mango, and sapota peels, utilising Gas Chromatography Tandem Mass Spectrometry (GCMS/MS) and Orbitrap High Resolution Liquid Chromatography Mass Spectrometry (Orbitrap HRLCMS). GCMS/MS characterisation of the volatile compounds revealed distinct variations: pineapple peels were dominated by organic acids (octanoic, nonanoic and heptanoic acids) and fatty acid esters such as hexadecenoic acid ethyl ester, banana and mango peels shared similar terpenes and alcohols including D-limonene, cyclohexanol, 1-methyl-4-(1-methylethyl)-, levomenthol, and dl-menthol, while mango peels specifically exhibited 𝛼-pinene, 𝛼-myrcene, and cis-13-octadecenoic acid. Similarly, the volatile profile of sapota peel was characterised by markers such as hydroperoxide, 1-ethylbutyl, 2-hydroxy-naphthalenecarboxaldehyde, lup-20(29)-en-3-ol, acetate, (3á)- and farnesyl bromide. Non-volatile profiling via Orbitrap HRLCMS identified organic acids and secondary metabolites, including gulonic acid, citric acid, 3-hydroxy-2H-pyran-2-one, and isocitrate in pineapple, dopamine, guanidinosuccinic acid, and ngamma nitro-L-arginine in banana, homomangiferin, (R)-mevalonic acid, and scutellarein 5,6,7,4'-tetramethyl ether in mango, and 5-keto-D-gluconate, lonchocarpenin, garcimangosone A and asparagoside B in sapota peels. The results represent that the specific fruit cultivar significantly modulates both qualitative and quantitative distribution of these bioactives. These findings establish a metabolomic framework for the targeted valorisation of these fruit wastes into value added functional foods and beverages.