Mango (Mangifera indica L.) is a tropical climacteric fruit that encompasses a myriad of metabolites mediating for its nutritive value, unique taste, flavor, and medicinal uses. Egypt is among the top mango producers worldwide, albeit little characterization has been made toward its fruits’ chemical composition. This study aims to assess metabolites difference via comparative profiling and fingerprinting of Egyptian mango in context to its cultivar (cv.) type and/or growth province. To achieve such goal, hyphenated chromatographic techniques (UPLC/MS) and UV spectroscopy were employed and coupled to multivariate data analysis for Egyptian mango fruits’ classification for the first time. UPLC/MS led to the detection of a total of 47 peaks identified based on their elution times and MS data, belonging to tannins as gallic acid esters, flavonoids, xanthones, phenolic acids and oxylipids. UV/Vis spectra of mango fruits showed similar absorption patterns mostly attributed to the phenolic metabolites, i.e., gallic acid derivatives and phenolic acids showing λmax at ca. 240 and 270 nm. Modeling of both UPLC/MS and UV data sets revealed that cv. effect predominated over geographical origin in fruits segregation. Awees (AS) cv. showed the richest phenolic content and in agreement for its recognition as a premium cv. of mango in Egypt. Results of total phenolic content (TPC) assay revealed that AS was the richest in TPC at 179.1 mg GAE/g extract, while Langara from Ismailia (LI) showed the strongest antioxidant effect at 0.41 mg TE/g extract. Partial least square modeling of UV fingerprint with antioxidant action annotated gallates as potential contributor to antioxidant effect though without identification of exact moieties based on UPLC/MS. The study is considered the first-time investigation of Egyptian mango to aid unravel phytoconstituents responsible for fruits benefits using a metabolomics approach.