Drought represents significant environmental stress, and improving agriculture water management and yield is a priority goal. The effect of diminishing soil water content in the grain filling (GF) stage, throughout physiological maturity (GM), on the yield and grain quality, leaf water potential (LWP), and maximum quantum yield (Fv/Fm) in four long photoperiod quinoa genotypes was evaluated in the South-Central zone of Chile, during the 2014–2015 and 2015–2016 seasons. Five irrigation treatments (T) were established. Irrigation was carried out when the available water (AW) of the root zone reached values of 100%, 70%, 40%, 20%, and 0%. The lowest LWP values were obtained by T20 and T0 (−1.95 MPa). The ‘Morado’ genotype reached the lowest LWP at both seasons, while the highest average LWP was achieved by the ‘AG 2010’ (2014–2015) and ‘Cahuil’ genotypes (2015–2016). A global trend of Fv/Fm values was observed from GF to GM: 0.74 toward 0.79 (2014/2015), and 0.74 toward 0.82 (2015/2016). Only during the second season, Fv/Fm showed differences among irrigation treatments. Total average grain yields in the second season (2.97 t ha⁻¹) were greater than those in the first season (1.43 t ha⁻¹). In both seasons, the ‘Cahuil’ genotype and T100 reached the highest yields. A significative decrease in yield was observed when AW diminished. A direct relationship between seed yield and leaf water potential (ΔY/ΔLWP) was found in all genotypes, varying between 5.53 (‘Cahuil’) and 2.86 t ha⁻¹ MPa⁻¹ (‘AG 2010’). Total proteins, albumins, and globulins varied between seasons, with almost no differences among irrigation treatments. Only the ‘Morado’ genotype showed a slight trend to obtain a higher content of total protein in both seasons. It is possible to grow quinoa under irrigation deficit conditions between GF throughout GM, maintaining yield parameters and nutritional quality.

The increasing water scarcity affects the agricultural sector, and it is a significant constraining factor for crop production in many areas of the world. Water resource management and use related to crop productivity is the most important factor in many crops. Since consumer demands healthy food, the nutritive quality and the active ingredient need to be considered within the productive issue. The objective of this study was to determine water technical efficiency related to seed yield and seed protein content and composition in quinoa (Chenopodium quinoa Willd.) under water stress using data envelopment analysis (DEA). The study was conducted in Chillan, Chile in two growing seasons. As water availability increased, seed yield, globulin, and albumin yield increased, particularly in the genotype Cahuil. The higher average efficiency levels for the DEA were 46.7% and 39.2% in Cahuil in both seasons at 20% available water (AW). The highest average efficiency of globulin yield was recorded in the same genotype (Cahuil). The highest multi-product technical efficiency levels in all input and output included in this study were observed in Cahuil, Regalona, and Morado under water scarcity in both seasons. In future studies related to crop management, DEA provides a good framework for estimating efficiency under restricted factors and multi-product results.