ABSTRACT Flavonoids are probable major contributors to the radical scavenging activity in Ecuadorian quinoa leaves, both from the bitter genotype (Chimborazo) and sweet varieties. In this study, we extracted these compounds using a simple, rapid (10 min), and environmentally friendly method based on deep eutectic solvents (DES). Extractions were performed in a ball mixer mill at room temperature with a eutectic mixture of choline chloride—glycerol—water at a molar ratio, of 1:2:1 and compared with classical methanol extraction. Both extracts were characterized using high‐performance thin‐layer chromatography and liquid chromatography‐tandem mass spectrometry‐based methods. Regardless of the type of solvent used (conventional or green solvent), quercetin and kaempferol glycosides were found as the major flavonols in sweet and bitter quinoa leaves. DES extract contains a higher amount of quercetin glycosides than methanol and shows a higher capacity to stabilize the quinoa radical scavengers compared to conventional solvent (liquids extracts—conservation for up to 4 months at 5°C). The present research indicates that DES represent an efficient green media for the stabilization of phenolic compounds from quinoa leaves and has the potential as a possible alternative to organic solvents. Our work opens new perspectives for the development of high‐added value products based on quinoa leaves for pharmaceutical, nutraceutical and agro‐food applications.