Mahlab cherry (Prunus mahaleb L.) is a plant native to the Mediterranean basin and Eastern Europe, with several health benefits and culinary uses. We explored the compositional heterogeneity in the aroma profile and nutrients of three P. mahaleb seeds in the context of its cultivar type, i.e., white and red, and in response to roasting. A holistic untargeted metabolomics approach was employed for the first time using solid-phase microextraction (SPME–GC–MS) profiles of seed volatiles and primary metabolites coupled with chemometrics. Around 65 peaks belonging to sugars, fatty acids, esters and organic acids were identified by GC–MS. White mahlab from Egypt is rich in fatty acids, e.g., oleic and α-linolenic acids. Some acyl esters, e.g., glycerylmonostearate and n-butylcaprylate, characterized mahlab cultivars from various origins. A total of 135 volatiles were identified, with organic acids and aldehydes the most abundant. Aldehydes were the most discriminatory in seed origin and in accounting for its distinct aroma. Several roasting indices were identified, viz. 1-octanol, γ-caprolactone and isomintlactone. A direct relationship between furans and fatty acids was rationalized by cyclic transformation of the latter into furan derivatives. This study provides the first chemical evidence supporting the nutritional and flavor determinants of mahlab seeds, suggesting novel uses as a functional food.