Although, the covalent modification of proteins with phenolic compounds has currently found great efforts, applications of these proteins are rare. Therefore, this study was planned to characterize the whey protein isolate (WP) modified with chlorogenic acid (CA) and rosmarinic acid (RA), at pH 9 in the presence of air and at room temperature. The modified protein was evaluated as antioxidant and antiviral agent to inhibit Tobacco mosaic virus (TMV) on infected tomato plants. The WP proteins were characterized using the change in the intensity of tryptophan fluorescence and UV-Vis spectra of proteins, RP-HPLC, ultra-high-performance liquid chromatography coupled with electrospray ionization-quadrupole-time of flight-mass spectrometry (UHPLC-ESI-Q-TOF-MS) and TEAC assay. The results showed that the maximal tryptophan fluorescence intensity of modified proteins, WP-CA and WP-RA, were significantly decreased by 54.71 % and 82.61%, respectively. Data of ESI-MS illustrated that one or more molecules of CA and RA covalently bound to WP. Moreover, the WP modified with RA showed better antioxidant activity when compared with the unmodified WP and WP modified with CA. The antiviral results indicated that plants treated with WP, WP-CA and WP-RA had a decreased number of local lesions and virus concentration over the controls. Quantitative real-time PCR analysis revealed that the expression levels of defense related genes, PR1 and phenylalanine-ammonia lyase (PAL) were significantly increased in treated tomato plants compared to the control. These results indicate that the modified proteins could be used to design a wide range of food products and at the same time improve the antiviral activity against TMV, which seriously harms the tomato crop and thus the manufacture of its products.