The roller milling of sorghum and quinoa seeds into flour fractions (coarse, middle, and fine) was investigated, chemically analysed, and applied in the baking of gluten-free sourdough bread. The gap settings were adjusted to 0, 5, 8, and 10 for quinoa, and 3, 5, and 7 for sorghum. The fine fractions reached values of up to about 41% (gap 8) for quinoa and around 20% for sorghum (gap 5). SEM pictographs illustrated the clear separation of each fraction with the chemical analysis showing high contents of protein, TDF (total dietary fibre), and IDF (insoluble dietary fibre) in the coarse fraction. Up to 77% starch content was obtained in the fine fraction with significant amounts of SDF (soluble dietary fibre), which has good health benefits. Increasing the dough moisture up to 90% helped in decreasing the bread crumb firmness, while low Avrami parameters and RVA pasting behaviour indicated a slow bread-staling rate for both sourdough breads.