This study explores how atmospheric cold plasma (CP) modulates the nutritional and allergenic properties of Atlantic cod through structural protein alterations. CP at 10 min reduced parvalbumin content by 9.14%, likely via α-helix loss and β-sheet increase (confirmed by FTIR amide I shifts and CD analysis), which may hinder IgE epitope recognition. Antioxidant indices TAC, TFC, and TPC peaked at CP10 (21.56%, 68.48%) and CP30 (14.00%), respectively. Protein content increased by 10.76% (pre-digestion) and 30.20% (post-digestion) at CP20, while peptide release rose by 61.18% and 26.27% at CP30. Despite microstructural and conformational changes, digestibility remained stable. These findings highlight CP as a non-thermal strategy that enhances bioactive and hypoallergenic properties of cod, with potential for broader application to other high-allergen aquatic proteins.