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Climate change scenarios predict that an extended period of drought is a real threat to food security, emphasizing the need for new crops that tolerate these conditions. Quinoa is the best option because it has the potential to grow under water deficit conditions. There is considerable variation in drought tolerance in quinoa genotypes, and the selection of drought-tolerant quinoa germplasms is of great interest. The main goal of this work is to evaluate the crop yield and characterize the physiology of 20 quinoa genotypes grown under water deficit in a wirehouse. The experiment was a complete randomized design (CRD) factorial with three replications. Seedling growth, i.e., fresh weight (FW), dry weight (DW), root length (RL), shoot length (SL), relative growth rate of root length (RGR-RL), shoot length (RGR-SL), and physiological performance, i.e., chlorophyll content (a and b), carotenoid, leaf phenolic content, leaf proline content, membrane stability index (MSI), and leaf K+ accumulation were evaluated in a hydroponic culture under different water-deficit levels developed by PEG 6000 doses (w/v) of 0% (control), 0.3%, and 0.6%. Yield attributes were evaluated in a pot at three different soil moisture levels, as determined by soil gravimetric water holding capacity (WHC) of 100 (control), 50% WHC (50 % drought stress) and 25% WHC (75% stress). In both experiments, under the water stress condition, the growth (hydroponic study) and yield traits (pot study) were significantly reduced compared to control treatments. On the drought tolerance index (DTI) based on seed yield, genotype 16 followed by 10, 1, 4, 5, 7, and 12 could be considered drought-tolerant genotypes that produced maximum grain yield and improved physiological characteristics under severe water stress conditions in hydroponic culture. In both studies, genotypes 3, 8, 13, and 20 performed poorly and were considered drought-sensitive genotypes with the lowest DTI values under water-stressed conditions. All the studied agronomic traits (grain yield, root and shoot length, shoot fresh and dry weights) and physiological traits (leaf phenolic, proline content, carotenoid, K+ accumulation, membrane stability index, and relative water content) were firmly inter-correlated and strongly correlated with DTI. They can be regarded as screening criteria, employing a large set of quinoa genotypes in a breeding program.