The goal of this study was to assess nutrient primary metabolites and aroma determinants in Prunus armeniaca L. fruits and seed kernels grown in Egypt represented by its different cultivars and agricultural conditions i.e., two different soil types (muddy versus sandy). Two techniques were employed to assess non-volatile and volatile metabolites using gas chromatography mass-spectrometry (GC-MS) post silylation, and headspace solid-phase micro-extraction (HS-SPME) coupled GC-MS, respectively. A total of 36 peaks belonging to sugars, fatty acids/esters and organic acids were identified by GC–MS in various apricot fruits and seed kernels cultivars. Glucose and sucrose were enriched in apricot fruits compared to the seed kernels. A total of 70 volatiles were identified, with lactones, alcohols and esters representing the main classes of apricot volatiles accounting for its discrete aroma. (E)-Anethole, β-ionone, γ-decanolactone and methyl palmitate were the major peaks contributing to the discrimination between various fruit cultivars and providing novel insight on apricot metabolome.