Dough quality and baking performance of wheat dough are significantly affected by the qualitative and quantitative composition of the gluten. Therefore, the degradation was studied of specific fractions of gluten proteins in sourdough as affected by starter cultures. Doughs were fermented for 0, 5, and 24 h at 30 °C after addition of Lactobacillus sakei, L. plantarum, L. sanfranciscensis or Enterococcus faecalis. Chemically acidified doughs were used as controls. All doughs were analyzed quantitatively for their content of albumins, globulins, gliadins, glutenins, and glutenin macropolymer by means of a combined extraction/HPLC procedure. Protein degradation during sourdough fermentation was primarily due to acidic proteases present in flour. While L. sakei, L. plantarum and L. sanfranciscensis were mostly non-proteolytic, E. faecalis clearly contributed to gluten proteolysis. Single gluten protein types were clearly different in their resistance to proteolytic activities of the dough system and E. faecalis, and, in contrast to total glutenins, the amounts of gluten macropolymer were significantly reduced already after 5 h of incubation. When longer fermentation times were applied, gluten was substantially degraded. The strongest decrease was found for the glutenin fraction leading to an increase of alcohol soluble oligomeric proteins in the gliadin fraction. The extent of the decrease of monomeric gliadins was strongest for the γ-type followed by the α- and the ω-types. This indicates that dough properties residing in specific types of gluten fractions can be influenced by the duration of fermentation and the application of proteolytic strains.