Quinoa is a pseudocereal from South America that has received increased interest around the world because it is a good source of different nutrients and rich in antioxidant compounds. Thus, this study has focused on the effects of different agronomic variables, such as irrigation and salinity, on the phenolic and saponin profiles of quinoa. It was observed that irrigation with 25% of full water restitution, with and without the addition of salt, was associated with increases in free phenolic compounds of 23.16 and 26.27%, respectively. In contrast, bound phenolic compounds were not affected by environmental stresses. Saponins decreased if samples were exposed to drought and saline regimens. In situations of severe water deficit, the saponins content decreased 45%, and 50% when a salt stress was added. The results suggest that irrigation and salinity may regulate the production of bioactive compounds in quinoa, influencing its nutritional and industrial values.