Pomegranate juice (PJ) constituents have shown to exhibit anticarcinogenic, antimicrobial, antioxidant and antiviral activities. In the present study, the concentration of phenolic compounds and the antiradical activity of PJs from the fruits of two relatively new Greek cultivars “Persephone” and “Porphiroyeneti” were determined in comparison to “Wonderful” cultivar. Total phenolic content and antiradical activity of the examined juices were found to vary in the same manner, decreasing as follows: “Porphiroyeneti”>“Wonderful”>“Persephone”. Antimicrobial activity of PJs was also determined showing equal or higher effect than commercial antimicrobial agents (streptomycin, ampicillin, bifonazole and ketoconazole). All tested extracts demonstrated noteworthy antibacterial activity with minimal inhibitory concentration ranging from 0.05 to 0.20 mg/mL and minimal bactericidal concentration ranging from 0.10 to 0.40 mg/mL. Also, PJ extracts showed satisfactory fungistatic (0.05-0.2 mg/mL) and fungicidal (0.1-0.3 mg/mL) activity against all fungi tested. Concerning the cultivars tested “Porphiroyeneti” showed slightly better antiradical and antimicrobial activity. In addition, a GC–MS methodology was developed for the determination of the phenolic profile of the PJ’s extracts after different types of chemical hydrolysis. Finally, an HPLC–PDA–ESI–MSn analysis was conducted for the identification of the phenolic compounds in the PJ’s extracts. In total, more than 30 non-anthocyanidinic and more than 20 anthocyanidinic compounds were identified. Our results confirm the functionality of pomegranate juices and the potential applications of PJ extracts towards novel products as food additives or preservatives.