Three Allium vegetables, Welsh onion from Okinawa, and Wakegi from Okinawa and Nagasaki were subjected to salinity-stress using seawater. The K⁺/Na⁺ ratio of the three Allium vegetables clearly decreased; however, there was no significant effect on growth parameters. Of the three Allium vegetables, 10% seawater treatment of Welsh onion and Wakegi from Nagasaki clearly enhanced both the sugar content and antioxidant activity. Therefore, seawater treatment may be potentially useful for the development of value-added Allium vegetables, enhancing the palatability and food functionality.