We investigate the effect of cold atmospheric plasma (CAP) on the native and glycated glutathione peroxidase 1 (GPx1) as the key antioxidant enzyme. We evaluate the role of reactive species, that is, reactive oxygen species and reactive nitrogen species, in the chemical modifications of proteins through controlling the surrounding gas of the helium plasma jet. The results show CAP has a great effect on both the structure and function of glycated GPx such that after a 600 s plasma treatment at 20 mm distance, enzymatic activity increases up about 51, 30, 25, and 2% for oxygen, air, argon, and nitrogen surrounding gas, respectively. Circular dichroism (CD) and fluorescence spectroscopies have been used for monitoring the structural and conformational alteration, and enzymatic activity measurement has also been performed as function analysis. The Maillard-related fluorescence of glycated protein is quenched after the CAP treatment, and CD spectra of secondary structure are shifted toward the native GPx. The findings of the present study represent a significant first step in the modification of glycated proteins by plasma for biomedical applications in diabetes treatment.