Lactobacillus plantarum ATCC 8014 was used to ferment quinoa flour, in order to evaluate its influence on the nutritional and rheological characteristics of both the sourdough and muffins. The quantification of carbohydrates and organic acids was carried out on a HPLC-RID system (high-performance liquid chromatography coupled with with refractive index detector), meanwhile HPLC-UV-VIS (high-performance liquid chromatography coupled with UV-VIS detector), AAS (Atomic absorption spectrophotometry), aluminum chloride colorimetric assay, Folin–Ciocalteu, and 1,1-Diphenyl-2-picrylhydrazyl radical scavenging activity (DPPH) methods were used to determine folic acid, minerals, flavonoids, total phenols, and radical scavenging activity, respectively. Two types of sourdough were used in this study: quinoa sourdough fermented with L. plantarum ATCC 8014 and quinoa sourdough spontaneous fermented. The first one influenced the chemical composition of muffins in terms of decreased content of carbohydrates, higher amounts of both organic acids and folic acid. Furthermore, higher amounts of flavonoids, total phenols and increased radical scavenging activity were recorded due to the use of Lactobacillus plantarum ATCC 8014 strain. These results indicate the positive effect of quinoa flour fermentation with the above strain and supports the use of controlled fermentation with lactic acid bacteria for the manufacturing of gluten free baked products.