Exploiting the relationship between the nutritional properties of seeds and the genetic background constitutes an essential analysis, which contributes to broadening our knowledge regarding the control of the nutritional quality of seeds or any other edible plant structure. This is an important aspect when aiming at improving the nutritional characteristics of crops, including those of Chenopodium quinoaWilld. (quinoa), which has the potential to contribute to food security worldwide. Previous works have already described changes in the nutritional properties of quinoa seeds due to the influence of the environment, the genotype, or their interaction. However, there is an important limitation in the analyses carried out, including the outcomes that can be translated into agronomical practices and their effect on seed quality. In the present study, several seed nutritional-related parameters were analyzed in 15 quinoa cultivars grown in a particular environmental context. Important agronomical and nutritional differences were found among cultivars, such as variations in mineral or protein contents and seed viability. More importantly, our analyses revealed key correlations between seed quality-related traits in some cultivars, including those that relate yield and antioxidants or yield and the germination rate. These results highlight the importance of considering the genotypic variation in quinoa when selecting improved quinoa varieties with the best nutritional characteristics for new cultivation environments.