The object of this study was to determine the phenolic profile, the total phenolic content and antioxidant capacity of pomegranate wine and compare to multi-varietal red wine using different spectrophotometric and spectrometric techniques. Total phenolic content was determined by the Folin-Ciocalteu assay. The antioxidant capacity was measured by the DPPH and the ABTS radical scavenging assays. The radical-scavenging capacity was higher for pomegranate wine (statistically significant difference was observed for the DPPH assay) in agreement with its higher total phenolic content (383.19 ± 18.22 and 296.57 ± 25.23 mg gallic acid equivalents/100 mL for pomegranate and grape wine respectively). Customized HPLC-PDA-ESI-MSn and GC-MS methods were applied for the identification and chemical characterization of the phenolic compounds for both wines. Identification using LC-MS was based on their λmax (nm) and the characteristic fragments which derived from the sequential fragmentation in MS while GC-MS was based on commercial libraries and mass spectra of authentic standards. Eighty one different phenolic compounds were characterised by LC-MS and one hundred eight compounds by GC-MS after different chemical hydrolysis regimes. The study signifies the prior treatment with alkaline hydrolysis which had a considerable effect on the detection of phenolic compounds. The results showed that the combination of LC-MS and GC-MS methods allowed the detection of different compounds while results from both techniques are complementary and may confirm each other. Phytochemicals with proven biological activities including antimicrobial, antiviral and chemoprotective, have been identified mainly in pomegranate wines. Furthermore, a significant diversity between pomegranate and grape wines was observed, in terms of their phenolic content and antioxidant profiles indicating the-nutritive and health-promoting effects of pomegranate wine.