Owing to the increasing role of fiber-rich wholegrain products in food preparation, it is necessary to determine the optimal ratio of protein to fiber in wholewheat flour. The effects of organic and mineral N fertilizers on the protein content (PC) and total content of arabinoxylans and β-glucans (AX+BG) and their ratio (PC:AX+BG) were investigated here. The effect of this ratio on the dough quality of winter wheat ‘Fredis’ was evaluated. The field experiment was conducted at the Estonian University of Life Sciences in 2014‒2017. The results showed that the total amount of AX+BG was significantly affected only by weather conditions (air temperature and precipitation). Higher total AX+BG was associated with higher water absorption capacity, longer dough development time, and a higher quality number of the dough. Better dough quality indicators were obtained when the PC:AX+BG ratio was in the range of 2‒2.2:1. The value of the PC:AX+BG ratio depended more on fiber content than on PC, because the variation in fiber values between trial years was up to three times greater than that of PC. Better dough quality was obtained from N treatments with higher organic and mineral N amounts and in years with lower or average grain yield.