Date palm (Phoenix dactylifera L.) is a globally edible fruit and a traditional dietary component in various cultures. The fruit’s fleshy part is consumed for its nutritional value, while the seeds are discarded or valorized for oil production and as a coffee substitute. The current study aimed to investigate date seeds’ metabolome, in addition to macro- and micro-elements composition within12 major Egyptian cultivars (cvs.) for the first time using gas chromatography coupled with mass spectrometry (GC-MS). Post-silylation GC-MS analysis and headspace coupled with solid-phase microextraction (HS-SPME) were used for nutrients and aroma profiling in roasted seeds, respectively. Furthermore, multivariate data analyses were employed for samples classification and markers identification via principal component analysis (PCA) and orthogonal projection to least square discriminant analysis (OPLS-DA). Models are further validated by permutation test. Moreover, absolute quantification of potential markers was attempted based on reference standards A total of 101 and 65 nutrient and aroma metabolites were annotated, respectively. Fatty acids/esters (38 peaks), sugars (18), organic acids (17), sugar alcohols (7), steroids/triterpenoids (5), alcohols and aldehydes (6), in addition to flavonoids (1) and phenolic acids (3) were identified as major components in GC-MS post-silylation platform. ‘’Khalas’’ cv. seed appeared the most nutritive being enriched in sugars and fatty acids/esters. Moreover, date seed volatiles from different cvs. were dominated by fatty acids/esters (19 peaks), esters (6), and phenols/ethers (9). Anethole (peak 47) was the most abundant at 9.1–23.3% of seeds contributing to their unique aroma, especially ‘’Barhi’’ a premium date cv. PCA score plot of primary metabolites’ dataset revealed for 1-monopalmitin and monostearin as potential markers for ‘’Aref’’ and ‘’Khalas’’. Furthermore, ‘’Barhi’’, ‘’Omeldehn’’, and ‘’Lolo’’ cvs. showed comparable aroma profile and in partial agreement with nutrient results. OPLS-DA model revealed that anethole, estragole, methyl esters of dodecanoic acid and octanoic acid were characteristic in case of ‘’Barhi’’ cv. which are likely to impart a fine aroma and flavor. With regards to minerals, ‘’Zamli’’, ‘’Barhi’’, and ‘’Hasawi’’ cvs. were most rich in calcium, copper, and selenium, respectively. This study offers new perspectives for the phytochemical makeup and valorization potentials of date palm seeds. Fatty acids/esters and sugars were the major components in date palm seeds found enriched in ‘’Khalas’’ cv, while anethole, estragole, methyl esters of dodecanoic acid and octanoic acid were potential markers of ‘’Barhi’’ cultivar. Such extensive profiling identified premium cvs. to be considered for food applications.