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Fruit extracts of Sambucus nigra L. (elderberry) and Punica granatum L. (pomegranate) have several applications in nutraceutical, cosmetics, and pharmaceutical industries thanks to their richness in antioxidant polyphenols, whose composition changes with the extraction method applied. We aimed to compare the efficiency of the fermentation extraction, recently applied by industries, with the ultrasound-assisted extraction–UAE, a well-known and efficient technique, on the yield of antioxidant polyphenols from elderberry fruits and pomegranate fruit-peels. Extracts were obtained by both methods, analyzed by high-performance liquid chromatography (HPLC) and the antioxidant capacities were evaluated using 2,2-diphenyl-1-picrylhydrazyl (DPPH) and Hydroxyl Radical Scavenging (HRS) assays. The main compounds detected in elderberry were caffeoyl and quercetin derivatives, present in higher amounts in UAE extracts. In pomegranate, punicalagin were the main constituents, also detected in higher contents in the UAE extracts compared to fermented ones. The UAE was more suitable for extracting anthocyanins from pomegranate. In addition, higher antioxidant capacities were observed in UAE extracts, possibly due to their richness in polyphenols. Therefore, despite the recent wide applicability and the good performance of the fermentation process, the UAE may be considered more efficient for the extraction of polyphenols from S. nigra and P. granatum fruits and may be used to obtain polyphenolic antioxidant extracts to be applied by several industries.