In order to promote breeding programs and a full reintroduction into production of two local red-fleshed apple varieties grown in Bekran and Bastam (Iran), the evaluation of their antioxidant properties was of interest. LC-MS(n) based metabolic fingerprinting analyses were applied to investigate the anthocyanin content of both peel and flesh components of the fruits. Cyanidin-3-O-hexoside isomers were present in both 'Bekran' and 'Bastam' apples, whereas 'Bekran' apple was a valuable source of anthocyanin rutinose derivatives. Employing DPPH(•), ABTS(•+), and ORAC methods, the antiradical efficacy was evaluated. The ability of the investigated fruit components to scavenge OH(•), and O(2) (•-) reactive species was also assessed. ID(50) values highlighted the massive antioxidant response of 'Bekran' peel component, able to counteract by 50 % OH(•), and O(2) (•-) at 130.3 and 91.6 μg/mL, respectively. The cytoprotective screening towards HeLa, HepG2, A549, SH-5YSY, and SK-N-BE(2)-C cell lines evidenced that the investigated Iranian red-fleshed apple fruits were able to exert a significant antioxidant response in hydrogen peroxide oxidized cell systems. Data collected suggested that the revaluation of 'Bekran' and 'Bastam' apple cultivars could represent a precious source of antioxidant compounds whose dietary intake could improve the human well-being reducing risks of free radical related chronic and degenerative diseases.