Saponins (SAPs) are a diverse family of plant secondary metabolites and due to their biological activities, SAPs can be utilised as biopesticides and as therapeutic compounds. Given their widespread industrial use, a search for alternative sources of SAPs is a priority. Quinoa (Chenopodium quinoa Willd) is a valuable food source that is gaining importance worldwide for its nutritional and nutraceutical properties. SAPs from quinoa seed coats could represent a new sustainable source to obtain these compounds in high quantities due to the increasing production and worldwide expansion of the crop. This research aims to characterise saponins of seed coat waste products from six different quinoa varieties for their potential use as a saponin source. Gas chromatography (GC)- and Liquid chromatography (LC)- with mass spectrometry (MS) were applied for qualitative and relative quantitative analysis of saponins. GC–MS led to the identification of three main aglycones, oleanolic acid (Ole), hederagenin (Hed), and a phytolaccagenic acid (Phy), while LC–MS enabled characterization of 24 SAPs with varying sugar moieties. Hed was the most abundant aglycone, followed by Phy and Oledepending on the genotype. Saponin distribution and relative abundances are discussed in the light of genotype provenance and agronomic features. Improved knowledge on the phytochemicals present in quinoa varieties might help in finding valuable and sustainable uses for quinoa SAPs in agroindustry as biopesticides as well as in the production of food and pharmaceuticals.