Date palm fruits of the species Phoenix dactylifera exhibit a great diversity in sensory attributes including skin color, smell and taste. This study attempts to elucidate the primary and secondary metabolite profiles of 21 date varieties from Egypt. A major difficulty is sugar rich matrix and skin-fibers embedding the secondary metabolites. A total of 49 metabolites extracted from the fruit skin were evaluated in a UPLC/PDA/ESI–qTOF-MS based metabolomics study. The total phenolic contents of the varieties varied from 233 to 1897mg/100g (2.3–19g/kg) dry weight. The predominant flavones were glycosides of luteolin and apigenin, quercetin conjugates were the principal flavonols, whereas caffeoyl shikimic acid was the main hydroxycinnamic acid conjugate. Aside from these major phenolic classes, a group of sphingolipids, fatty and other organic acids was also identified. The total non-fatty organic acid content correlates with reported shelf lives. GC–MS was further utilized to localize primary metabolites in fruits (i.e. sugars and organic acids) with glucose and fructose accounting for up to 95% of TIC among most varieties. Principal component and clustering analyses reveal that flavonols and sugars, both contribute the most to variety classification. This study provides the most complete map for polyphenol & sugar distribution in Egyptian date fruit varieties. By describing the metabolite profiles in a diverse dataset of P. dactylifera, this study provides the basis for future investigations of date fruit nutritional value beyond providing energy and its potential for nutraceutical enhancement or storability.