Currently, there is an increase in consumer interest in food produced from raw materials from organic farming, which has an impact on the greater attention paid to the possibility of increasing the cultivation of old cereal species. One of the cereals that is suitable for these trends is mountain rye, which is a premise for undertaking research on the usefulness of this cereal grain in food production. Therefore, the aim of the study was to compare the baking value of flour with different milling yields obtained from milling mountain rye grain. The research material consisted of rye grain (Secale montanum Guss.), which was milled, and 6 different rye flours were obtained. The flour was tested for selected quality parameters such as moisture, crude protein content, total ash content, and acidity. Doughs were prepared and fermented using a single-phase method carried out in two different variants, with or without the addition of lactic acid. The obtained rye breads were quality assessed and subjected to organoleptic and consumer evaluations. The use of the fermentation method with dough acidification with lactic acid allowed us to obtain breads with a better specific volume and acidity compared to those obtained from dough without acidification. Breads baked from dough prepared using the method of non-acidification with lactic acid had better porosity of the crumb. In the quality classification, breads made from low-extract flour turned out to be the best, and breads baked from dough made using the non-lactic acid acidification method were more generally accepted by panelists. As confirmed by research, mountain rye grain is a raw material for the production of flour with good baking value, which depends on the preparation of the grain and milling method. The quality of rye bread made from mountain rye flour depends on the flour yield, the baking value of the flour, and the method used for dough fermentation for bread baking.