Sprouts consumption is increasing worldwide due to their nutritional and health benefits. However, they can be sources of foodborne bacterial diseases, including sprout-related outbreaks caused primarily by Shiga toxin-producing Escherichia coli and Salmonella spp. The aim of this study was to determine the efficacy of a dried sea buckthorn fruit extract in sanitization of contaminated radish seeds. The efficacy of 15-min seed treatment and 3-h soaking in the extract solution was evaluated in comparison to the treatment with 20,000 mg/L calcium hypochlorite, recommended by the U.S. Food and Drug Administration. The effect of the sea buckthorn fruit extract on radish seed germination capacity and the profile of phenolic compounds in the extract were also determined. Decontamination effect of the extract after a 15-min seed treatment ranged from 72.1% against Staphylococcus aureus to 93.0% against Listeria monocytogenes and was higher than that of active chlorine against E. coli, S. aureus and Salmonella enterica. Soaking seeds for 3 h in the extract increased the decontamination efficiency only against S. aureus (81.9%). Compared to water, after 4 days of sprouting, no significant differences were found in radish seed germination capacity and the length of roots and hypocotyls of sprouts. The sea buckthorn fruit extract had a high content of phenolic compounds, namely isorhamnetin 3-rhamnosylglucoside (12.99 mg/L), isorhamnetin 3-rutinoside (8.25 mg/L), protocatechuic acid (5.43 mg/L), isorhamnetin 3-glucoside (3.41 mg/L), and gallic acid (3.36 mg/L). The extract can be used as a substance limiting bacterial contamination of radish seeds and, as a result, sprouts, as well as a valuable source of phenolic compounds.