Gluten-free (GF) baked goods available in the market are often poor in nutrients, such as protein, dietary fibre, micronutrients and bioactive compounds, and have low technological quality. Therefore, it is important to develop GF products with nutrient-rich flours, like quinoa (Q) and buckwheat (BW). Sourdough (SD) technology generates desirable nutritional and technological effects to improve GF bread. The objective of this work was to evaluate the effect of four autochthonous strains of lactic acid bacteria used as sourdough starters on the nutritional and technological quality of GF breads made with non-conventional flours. Lactiplantibacillus plantarum T3, Limosilactobacillus fermentum T4, Pediococcus acidilactici 26 and Pediococcus pentosaceus 82 were isolated in Q and BW flours. Nutritional and technological properties of flours, SD and breads were evaluated. In Q SD and breads, there was a 90% increase of polyphenols, 36% of ferulic acid and 131% in antioxidant capacity with respect to control compared to BW. In Q BW SD and breads, there were higher amounts of free amino acids and lower phytic acid content compared to SD controls. The incorporation of SD increased the specific volume, reduced the initial firmness of the crumb and the rate of hardening, produced a darkening of the crust; the crumbs of the breads were spongier, with a greater fraction of air and quantity of alveoli. Breads with Q SD presented better technological quality than breads with BW SD. Lim. fermentum T4 and P. pentosaceus 82 produced SD and breads with better technological quality.