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Sea buckthorn carotenoids extracted using CO₂ supercritical fluids method were encapsulated within whey proteins isolate by transglutaminase (TG) mediated crosslinking reaction, coacervation and freeze drying. The encapsulation efficiency was 36.23 ± 1.58%, with β-carotene the major carotenoid present in the powder. The confocal analysis revealed that TG-ase mediated cross-linking reaction enhanced the complexes stability to such a manner that a double microencapsulation was performed. The powder showed an antioxidant activity of 2.16 ± 0.14 mMol Trolox/g DW and an antifungal activity against Penicillium expansum MIUG M11. Four variants of domestic ice creams were obtained, with a total carotenoids content variation of 1.63 ± 0.03 mg/g D.W. in sample with 2% powder and 6.38 ± 0.04 mg/g D.W. in samples with 4% extract, having satisfactory antioxidant activity. The storage stability …