The application of cold plasma (CP) treatment was investigated for its effectiveness in promoting the covalent grafting of β-lactoglobulin (β-LG) and epigallo-catechin 3 -gallate (EGCG), as well as improving the antioxidant capacity of β-LG and eliminating its antigenicity. The results indicated that CP treatment significantly enhanced the covalent grafting of β-LG and EGCG. The maximum EGCG content in β-LG-EGCG complexes reached 47.08 ± 0.58 mg/g (with 45 s treatment), as confirmed by SDS-PAGE analysis and FTIR spectroscopy. Additionally, LC-MS/MS identifies two binding sites (T76 and K77) of EGCG in the β-LG-EGCG conjugates. After 60 s treatments, there was a significant reduction in the IgG binding capacity of β-LG-EGCG conjugates (29.97 ± 0.05%). Further analysis suggested that the change in the conformational epitopes of β-LG, due to the conjugating with EGCG, was likely the main factor responsible for the reduced binding Immunoglobulin G (IgG) capacity. The maximum antioxidant activities of β-LG-EGCG conjugates were found to be 974.14 ± 1.94 μmol TE g−1 for ABTS and 748.48 ± 9.66 μmol TE g−1 for DPPH). These values represent an eightfold increase in DPPH activity and a twofold increase in ABTS compared to the control sample. This study demonstrated that the CP treatment is highly effective technology for facilitating the covalent grafting of polyphenols to proteins, thereby enhancing their antioxidant properties and eliminate their antigenicity.