Soil moisture stress has become a serious environmental limitation to crop productivity and quality. The root system is the first organ sensing the changes in soil moisture; therefore, root development under water deficit is an important indicator for plant's drought tolerance. Previous studies focused on quinoa varietal differences in morphological traits under water stress; however, variation in root development including both growth and diameter responses to drought remains largely unclear. We conducted a preliminary screening of a diverse set of 30 quinoa genotypes to evaluate genetic variation in growth and yield performance in response to drought stress. Variation in drought tolerance indices showed large variation across the quinoa collection. Based on these results, five genotypes representative of a range of drought tolerance levels including 2‐Want, Atlas, NL‐6, Pichamán and Sayaña were selected to evaluate root development under control and severe drought conditions. Inhibition of root development was found for all genotypes as compared to controls; however, significant variation in root growth response to drought stress was observed. Among genotypes, Atlas and 2‐Want expressed drought‐tolerant phenotypes. The analysis of the interrelations between genotypes root length, root diameter, root surface area, drought tolerance and geographical origins reveals interesting guidelines for further studies to explore the mechanisms behind quinoa roots adaptation to drought.