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Ice containing essential oils (EOs) nanoencapsulated in β-cyclodextrins (β-CD) (named as EOs+β-CD ice) was used for stunning/slaughtering by hypothermia in ice slurry, and for ice storage of gilthead seabream. Clove essential oil (CEO) was used at fish stunning/slaughtering, while ice storage of whole fish was performed using a combination of carvacrol, bergamot and grapefruit EOs (CBG). Inclusion complexes CBG+β-CD were characterized, and antimicrobial effect was also evaluated. The kneading method used to form inclusion complexes with CBG showed a good complexation efficiency. Microbial, physical-chemical and sensory analyses were carried out to assess the quality changes of fresh whole seabream during ice storage at 2 °C for 17 days. Results (microbial, chemical and sensorial) indicated that seabream stunning/slaughtering and storage using EOs+β-CD ice (in low doses of 15 mg/kg ice for stunning, and 50 mg/kg ice for ice storage) improved the quality of fresh fish and extended the shelf-life up to 4 days.