Non Celiac Wheat Sensitivity (NCWS) is an intolerance to wheat products and individuals with NCWS often adhere to a gluten free diet. However, gluten free diets are often associated with a reduced sensory and nutritional quality. Wheat Germ Agglutinin (WGA) is one of the wheat components linked to NCWS. This study explored the fate of WGA during sourdough fermentation. To assess the role of thiol-exchange reactions and proteolysis, sourdoughs were fermented with Fructilactobacillus sanfranciscensis DSM20451, F. sanfranciscensis DSM20451ΔgshR, which lacks glutathione reductase activity, or Latilactobacillus sakei TMW1.22, with or without addition of fungal protease. The conversion of WGA was determined by size exclusion chromatography of fluorescence-labeled WGA, and by enzyme-linked immunosorbent assay (ELISA). Commercial whole wheat flour contained 6.6 ± 0.7 μg WGA/g. After fermentation with L. sakei TMW1.22 and F. sanfranciscensis DSM20451, the WGA content was reduced (p < 0.05) to 2.7 ± 0.4 and 4.3 ± 0.3 μg WGA/g, respectively, while the WGA content remained unchanged in chemically acidified controls or in doughs fermented with F. sanfranciscensis DSM20451ΔgshR. Protease addition did not affect the WGA content. In conclusion, the fate of WGA during sourdough fermentation relates to thiol-exchange reactions but not to proteolytic degradation.