Quinoa has a high nutraceutical potential because of the presence of secondary metabolites called saponins, which have industrial and medicinal uses and protect against attacks by pathogens. These compounds are found especially in the seed coat and give the grain a bitter taste; therefore, they must be eliminated before consumption. Despite the potential use in Colombia, there are few studies aimed at quantifying this metabolite. Therefore, the objective of this research was to evaluate two extraction methodologies (physical and chemical) and two methods for quantifying saponins in five quinoa genotypes grown in Colombia. The most efficient extraction method was the physical method. The saponin contents of the five genotypes were variable. The cluster analysis differentiated the genotypes into two groups: low saponin content (<4.49 mg/g seed) and high saponin content (>14.76 mg/g seeds). Blanca de Jericó had the lowest saponin content (<0.40%), and Amarilla de Maranganí had the highest content (>0.18%). Identifying more efficient methodologies for extracting and quantifying saponins will allow a better characterization of the germplasm and selection of genotypes with desirable characteristics for both consumption and industrial use.