The present study showed that differences in climatic conditions, altitudes and maturity stages have profound influence on the bioactive compounds of pomegranate fruit (cv. Wonderful). The results also showed that (+)-catechin, (−)-epicatechin, naringin,gallic acid had high concentrations regardless of maturity stages.Pomegranate juice showed significantly higher antioxidant activity measured by FRAP which increased with advancing fruit maturity whereas RSA decreased. Higher vitamin C concentration was found in fruit harvested at medium (662 m) altitude, with lower total anthocyanin concentration than those from lower (222 m)and higher (898 m) altitudes at full ripe stage. In addition, principal component analysis showed that fruit harvested from three different altitudes varied significantly in concentration of metabolites.More specifically, fruit harvested at lower altitude characterized by the mediterranean climate had significantly higher metabolites especially total flavonoids, total anthocyanin, epicatechin, rutin,kaempferol-3--d-glucoside and protocatechuic acids followed by higher (subtropical climate) and medium (arid to semi-aridclimate), highlighting the importance of altitude and climatic condition of growing area on the biochemical composition of pomegranate cv. Wonderful. In addition, significant variation in phenolic content could be rooted in the maturity of the fruit during harvest since ripening is driven by temperature which varied significantly across the altitudes. It could be suggested that fruit did not mature simultaneously thus resulting in variation in the phenolic compounds investigated.