Cold atmospheric plasma (CAP) is an emerging technique that has drawn noticeable interest from food scientists. The aim of this study was to examine the extent of CAP effects on wheat flour gliadin and glutenin proteins. Both wheat flour and previously prepared gliadin and glutenin extracts were subjected to CAP treatment. Surface dielectric barrier discharge (SDBD) type of CAP treatment was used for the treatment of wheat flour (4 min). Additionally, the SDBD treatment was also performed on previously prepared glutenin and gliadin extracts (1 min). Proteins were chromatographically separated and the total amount of proteins, the amount of proteins within the fractions, and their relative concentrations were determined. The treatment leads to a decrease in the total amount of proteins, compared to the untreated samples, which is indicative of the depolymerization of gluten proteins, thereby reducing the amounts of large-sized protein polymers, indicating they reduced immunoreactivity. Novelty impact statement Cold atmospheric plasma (CAP) has drawn noticeable interest as a novel non-thermal processing technology. Nevertheless, studies on the CAP potential to modify the immunoreactivity of wheat proteins are sparse. The molecular weight distribution of wheat protein polymers was altered after CAP treatment and the decrease in the amount of proteins was observed compared to the untreated samples. The results show that the amount of proteins within the fractions responsible for allergenicity decrease after CAP treatment, which indicates that the CAP technique can be used for reducing wheat proteins allergenicity.