As the concentrations of essential vitamins and minerals and a number of other health‐promoting compounds are often low in stable crops, research is under way to understand and increase synthesis of phytochemicals in order to improve crop nutritional quality. The question addressed in this study is whether shoot genotypes or root genotypes with tolerant drought character are able to increase the fruit quality and production under moderate water stress. Zarina (drought tolerant) and Josefina (drought sensitive) were grafted self and reciprocally. The results showed that the use of cv. Zarina (drought tolerant) as rootstock (Zar × Jos) results in a greater number of fruits under water‐stress conditions, a moderate increase in some antioxidant compounds, such as ascorbic acid, phenols and flavonoids and lycopene and β‐carotene, and Zar × Jos showed high levels of sugars and organic acids, sweetness index and sugars : acids ratio, as well as important minerals, such as K and Mg, which could increase its nutritional quality under stress conditions. Overall, the use of drought‐tolerant rootstock could provide a useful tool to improve fruit yield and quality of cherry tomato fruit under moderate water stress, which in turn could mean lower costs in the use of irrigation water.