Secondary metabolites play fundamental roles in apple, influencing the interaction with pollinators and frugivores for seed dispersal, contributing to fruit quality and promoting human health through their antioxidant property. Domestication and breeding have significantly re-shaped the apple metabolism, altering both aromatic profiles and nutritional properties. This study assessed the secondary metabolite variation in a comprehensive Malus spp. collection comprising 163 accessions belonging to 44 species. The profiling of phenolic and volatile organic compounds (VOCs), performed with Ultra-Performance Liquid Chromatography (UPLC) and Proton-Transfer-Reaction Time-of-Flight Mass Spectrometry (PTR-ToF-MS) instruments respectively, in both skin and pulp tissues, uncovered distinct metabolic patterns between wild and domesticated apples. This investigation underlined the higher concentration of these metabolites in the skin tissue and revealed a clear metabolic divergence between the two groups of Malus accessions. Wild Malus spp. accessions resulted particularly rich in specific polyphenols characterized by antioxidant activity, including catechin and procyanidins. Conversely, apples of Malus domestica accessions exhibited a more abundant VOC profile, particularly represented by esters associated with fruity aroma, enhancing sensory appeal. These findings provide a foundation for leveraging wild germplasm in breeding programs, and the identification of accessions with high polyphenolic concentration and desirable aromatic profiles offers valuable opportunities to improve the aromatic and nutraceutical properties of apple.