The assortment and quality of bakery products designed for celiac patients may be improved by designing whole grain ingredients with low residual prolamin contents. The main objective of this study was to evaluate the extent of prolamin hydrolysis and pentosan solubilization in germinated-rye sourdoughs (GRSDs). Size-exclusion chromatography analyses, the fate of fluorescent prolamin, and immunological analyses determined the extent of prolamin hydrolysis and pentosan solubilization. Hydrolysis of rye prolamins was extensive in GRSDs, and according to enzyme-linked immunosorbent assay analyses, more than 99.5% of the prolamins were hydrolyzed. Pentosan solubilization occurred in native-rye sourdoughs, whereas in GRSDs, pentosans were partially hydrolyzed to monosaccharides. Test baking showed that the use of GRSD improved the overall quality of oat bread and that an estimated daily gluten intake from 100 g of bread would be less than 10 mg. However, the clinical safety must be assured before making any recommendations for celiac patients to use such products.