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Pomegranate juice has gained a high reputation for its health properties and consequently is now a highly demanded product. However, there is an interest in knowing if there are differences between conventional and organic agricultural practices. For that reason, total phenolic content, antioxidant capacity, punicalagin isomers and sensory analysis of pomegranate juices from Mollar de Elche cultivar were studied. A comparison between fresh and commercial pomegranate juice obtained by conventional and organic agricultural practices was conducted. The total phenolic content values ranged from 2285 to 2457 mg GAE L−1, however, there was no significant difference among conventional and organic juices. The antioxidant capacity evaluated by DPPH and ABTS methods showed significant differences (p &lt, 0.05) among conventional and organic juices. The antioxidant capacity values ranged from 17.7 to 35.9 mmol Trolox L−1 for DPPH and from 5.09 to 27.9 mmol Trolox L-1 for ABTS. Significant differences (p &lt, 0.05) were observed among conventional and organic juices in punicalagin isomer, with the highest value found in conventional fresh pomegranate juice (0.48 g L−1). Descriptive sensory analysis showed that fresh pomegranate, fresh rind, earthy, vegetal, bitter, and astringent notes were higher in conventional fresh pomegranate juice. Cooked and mushroom notes predominated in conventional commercial pomegranate juice, while the organic juice was characterized by fresh pomegranate, fresh rind, earthy and sweet notes.