Concentration and composition of storage proteins affect the baking quality of wheat. Although both are influenced by late nitrogen fertilization, it is not clear whether compositional changes are sufficient to improve the baking quality, and whether such effects are cultivar specific. In a pot experiment, two winter wheat cultivars belonging to different quality classes were supplied with two levels of late N fertilizer. Protein subunits were analysed by SDS-PAGE (Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis). Late N supply increased grain yield and protein content in both cultivars, but improved baking quality only in Discus, correlated with stronger changes in glutenin and gliadin fractions. Where baking quality was improved, this occurred at the lower late N level. Overall, the composition rather than the amount of gluten proteins was decisive for flour quality. Measures for enhancing grain protein concentration and composition are less necessary for cultivars such as Rumor in order to achieve optimum baking quality. These results open up an opportunity to reduce N fertilization in wheat production systems.