This study aimed to evaluate the effect of partial rye flour (RF) replacement with white bean malt (WBM) and red bean malt (RBM) on the baking and the nutritional quality of bread. The addition of white and red bean malts to the rye flour reduced the falling number and the maximum viscosity of the paste. Significant differences in the color of the crust and crumb of baked bread were shown. The addition of malt from bean seeds did not cause significant changes in the consumer assessment of bread. In some cases, a 30% increase in the polyphenols content was observed and an improvement in the antioxidant properties of bread with WBM and RBM was noted. Also, the overall protein and essential amino acids content in the bread was significantly increased. Due to WBM and RBM addition, the quantity of volatile compounds was higher than it was in the control sample, and in specific instances, it had doubled compared to the control sample.