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The degradation of the cereal proteins in wheat and rye sourdough fermentations strongly affects the quality of bread. Acidification and the reduction of disulfide bonds of gluten by heterofermentative lactobacilli increase the activity of cereal proteases and substrate accessibility; amino acids are accumulated by strain-specific intracellular peptidases of lactobacilli. Germinated cereals or other proteases enable an extensive degradation of proteins in sourdoughs in fermentation protocols that may be used to develop new products for individuals with gluten intolerance. The increased knowledge on proteolysis in sourdoughs enables a directed optimization of fermentation to improve bread quality.