A quinoa sourdough inoculated with Lactobacillus plantarum ATCC 8014 vs. a spontaneous sourdough were used to assess the changes in amino acid content released by proteolysis and the volatile derivatives formation in gluten-free muffins. Considerable increases, more than double, in leucine, isoleucine, histidine, lysine, γ-aminobutyric acid were recorded in gluten-free muffins obtained with the inoculated quinoa sourdough fermented for 24 h. Moreover, important markers of aroma compounds like 3-methylbutanal, 2-methylbutanal, 2.3-pentanedione, limonene were found in high and statistically different concentrations when the inoculated sourdough was used. The capacity of these volatiles to transfer pleasant taste and flavor (fruity, citrus, chocolate notes) was correlated with the results of the sensory analysis, clearly highlighting the high consumers' acceptability for gluten-free muffins obtained with inoculated sourdough. Quinoa fermentation by lactic acid bacteria could be a new alternative to produce gluten-free products enriched in amino acids and with good sensory features.