Iran has been faced to drought during last decades, and one way to overcome this phenomenon is to improve the water productivity by introducing new crops tolerant to water stresses such as quinoa. Two‐year field experiment was performed to find out the response of quinoa (cv. Titicaca) to deficit irrigation imposed at different growing stages. Hence, the effect of full irrigation (100% irrigation water requirement) and deficit irrigation (50% full irrigation) on physiological parameters, yield, irrigation water productivity and root density of quinoa was investigated during 2016 and 2017 growing seasons. The result showed that there was a significant difference between all variables in two years. Higher average air temperature in 2017 (2.0°C) resulted in a reduction of seed yield and water productivity (55% and 40% of that obtained in 2016, respectively). Application of deficit irrigation during different growing stages reduced crop height, stomatal conductance and seed yield, while it increased the root length density in both years. In conclusion, flowering stage of quinoa was very sensitive to deficit irrigation, and irrigation at grain filling stage would not help to recover the seed yield. Furthermore, the seed yield was lower than that obtained in other studies performed in other countries using same quinoa cultivar, which could be due to higher amount of applied irrigation water and different phenology under different climatic conditions. A decision on cultivating this crop under semi‐arid conditions has to be made considering limited water resources.