Wheat flour protein components affect the processing quality of wheat. While it is known that zinc (Zn) fertilization can change flour protein content, there is little knowledge about Zn influence on flour protein composition. A pot experiment was conducted with five Zn fertilization treatments and three wheat genotypes differing in protein concentration and gluten composition. Zn fertilization up to 10 mg Zn/kg soil increased activity of nitrate reductase and glutamine synthetase in flag leaves after flowering, but 40 mg Zn/kg soil caused a genotype-dependent decline in these activities. Similarly, an increase in Zn fertilization was associated with a genotype-dependent increase in grain protein content and concentrations of gliadins, glutenins, albumins and globulin in flour, followed by a decrease of all three protein types at 40 mg Zn/kg soil. These results demonstrate that Zn nutrition can alter flour protein content and composition in wheat that has differential end uses, influencing flour quality.