The importance of quinoa has been emphasized considerably in the recent decades, as a highly nutritional crop seed that is tolerant to salinity and amenable to arid agronomical conditions. The focus of this paper is to provide raw and a supplemental data of the research article entitled “Agronomic performance of irrigated quinoa in desert areas: comparing different approaches for early assessment of salinity stress”, aiming to compare different approaches for early detection, at the genotypic and crop levels, of the effect of salinity caused by irrigation on the agronomic performance of this crop. A set of 20 genotypes was grown under drip irrigation in sandy soil, amended with manure, at the International Center for Biosaline Agriculture (UAE) for two weeks, after which half of the trial was submitted to irrigation with saline water and this was continued until crop maturity. After eight weeks of applying the two irrigation regimes, pigment contents were evaluated in fully expanded leaves. The same leaves were then harvested, dried and the stable carbon and nitrogen isotope compositions (δ13C and δ15N) and the total nitrogen and carbon contents of the dry matter analyzed, together with ion concentrations. At maturity yield components were assessed and yield harvested. Data analysis demonstrated significant differences in genotypes response under each treatment, within all assessed parameters. The significant level was provided using the Tukey-b test on independent samples. The present dataset highlights the potential use of different approaches to crop phenotyping and monitoring decision making.