Currently it is estimated that the 20% of total cultivated land is affected by salt. Besides, drought events will increase worldwide. These factors are affecting plant growth and crop production compromising food security. Within this context, quinoa (Chenopodium quinoa) is becoming an alternative pseudocereal for food supply due to its capacity to grow under harsh environmental conditions. Besides, it is being proposed as key model species to study the physiological processes that permit this tolerance, although how N metabolism responds has been barely studied. This paper addresses, on one hand, the response of quinoa’s N metabolism (N uptake, translocation, reduction and assimilation) under the forthcoming climatic conditions and, on the other hand, the comparison of the effects of both stresses when plants have similar relative water content and photosynthetic rates. Under mild salt stress (120 and 240 mM NaCl) N assimilation is not affected, while the N uptake is favored. Under severe salt stress (500 mM NaCl), N uptake is reduced, decreasing leaf nitrate and protein concentration; nevertheless, leaf free amino acids are maintained –to perform osmotic adjustment–. N uptake rate is more affected under drought than under severe salt; furthermore, under severe salt stress, quinoa allocates more nitrogen to roots to finely regulate NO3− and Cl− uptake, while under drought it allocates more to leaves to ensure photosynthesis. These results indicate that quinoa’s N metabolism is tolerant to drought and salt stress, although the strategies of this species for coping with the aforementioned stresses are different.