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Caffeoylquinic (5-CQA) and feruloylquinic (5-FQA) acids, found in coffee and other plant sources, are known to exhibit diverse biological activities, including potential antioxidant effects. However, the underlying mechanisms of these phenolic compounds remain elusive. This paper investigates the capacity and mode of action of 5-CQA and 5-FQA as natural antioxidants acting as hydroperoxyl radical scavengers and xanthine oxidase (XO) inhibitors. The hydroperoxyl radical scavenging potential was investigated using thermodynamic and kinetic calculations based on the DFT method, taking into account the influence of physiological conditions. Blind docking and molecular dynamics simulations were used to investigate the inhibition capacity toward the XO enzyme. The results showed that 5-CQA and 5-FQA exhibit potent hydroperoxyl radical scavenging capacity in both polar and lipidic physiological media, with rate constants higher than those of common antioxidants, such as Trolox and BHT. 5-CQA carrying catechol moiety was found to be more potent than 5-FQA in both physiological environments. Furthermore, both compounds show good affinity with the active site of the XO enzyme and form stable complexes. The hydrogen atom transfer (HAT) mechanism was found to be exclusive in lipid media, while both HAT and SET (single electron transfer) mechanisms are possible in water. 5-CQA and 5-FQA may, therefore, be considered potent natural antioxidants with potential health benefits.