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This study was aimed at identifying new efficient antioxidant juniper species and their metabolites, which are responsible for this activity. About 30 juniper representatives were assayed for antioxidant activity (DPPH (2,2-diphenyl-1-picrylhydrazyl) and ABTS (2,2′-azino-bis(3-ethylbenzthiazoline-6-sulphonic acid) radical scavenging) and total polyphenol content (TPC). The most active species were identified, and their most abundant polyphenols were quantified by the LC-electrospray ionization (ESI)-MS/MS-multiple reaction monitoring (MRM) method. In the group of studied species, J. ashei (mountain cedar) leaf extract was outlined as the best antioxidant with the highest TPC. Catechin was revealed as the most abundant polyphenol in the J. ashei extract, contributing to its superior antioxidant properties. An in-depth analysis of antioxidant capacity was also performed. The higher metal-chelating activity was observed in the case of J. sibirica (0.83 mg DE/mL), whereas the lowest was observed for J. communis (3.2 mg dry extract (DE)/mL) extracts. All efficient antioxidant extracts were also able to inhibit lipoxygenase. EC₅₀ values ranged from 1.77 to 2.44 mg DE/mL. The most effective inhibitors were J. ashei and J. formozana extracts, which acted as uncompetitive lipoxygenase (LOX) inhibitors. The presented results have potential application in the pharmacy and cosmetics for the generation of antioxidant compositions based on naturally derived lead compounds for the prevention of oxidative-stress associated organ-degenerative diseases, cancer, or other free radical-induced disorders. Full article