Genotypic variations in leaf gas exchange and grain yield were analysed in 10 highland‐adapted quinoa cultivars grown in the field under drought conditions. Trials took place in an arid mountain region of the Northwest of Argentina (Encalilla, Amaicha del Valle, 22°31′S, 65°59′W). Significant changes in leaf gas exchange and grain yield among cultivars were observed. Our data demonstrate that leaf stomatal conductance to water vapour (gs) is a major determinant of net CO2 assimilation (An) because quinoa cultivars with inherently higher gs were capable of keeping higher photosynthesis rate. Aboveground dry mass and grain yield significantly varied among cultivars. Significant variations also occurred in chlorophyll, N and P content, photosynthetic nitrogen‐use efficiency (PNUE), specific leaf area (SLA), intrinsic water‐use efficiency (iWUE) and carboxylation capacity (An/Ci). Many cultivars gave promissory grain yields with values higher than 2000 kg ha−1, reaching for Sayaña cultivar 3855 kg ha−1. Overall, these data indicate that cultivars, which showed higher photosynthesis and conductances, were also generally more productive. Carbon isotope discrimination (Δ) was positively correlated with the grain yield and negatively with iWUE, but δ15N did not show significant correlations. This study provides a reliable measure of specific responses of quinoa cultivars to drought and it may be valuable in breeding programmes.