The aim of this work was to obtain sweet quinoa seeds by a pearling process. Thus, two different pearling degrees (20% and 30%) were tested. Moreover, the effect of pearling process on saponins and phenolic content in quinoa were evaluated. To this end, GC-MS methodology was used to identify and quantify the saponins and reversed phase-high performance liquid chromatography coupled to DAD and mass spectrometer detectors was applied to study the phenolic composition. As expected, whole quinoa had the highest saponins and phenolics contents. An abrasion degree of 30% was necessary to obtain sweet quinoa (with a total saponin content lower than 110 mg/100 g). Obviously, this process caused a decrease of 21.5% and 35.2% of free and bound phenolic compounds, respectively. However, this decrease was lower if compared with other cereals. Thus, pearling process is a promising sustainable method to obtain sweet quinoa with a "green" approach.