Citrus fruit is one of the most important commercial fruit crops in the world. It is essential to use citrus rootstocks in this crop, since all varieties, whether, oranges, tangerines, lemons and grapefruits are highly sensitive to Phytophthora spp., present in almost all soils. Selection of optimal rootstock is crucial for commercial cultivation of citrus fruit, as the effect fruit production, tree size, diseases, and adaptation to certain soil conditions. Besides, rootstock may affect internal quality parameters of citrus fruits, including juice total, soluble solids, acidity, antioxidant capacity, sugars and organic acids content, flavor. In this study, we evaluated the effect of three rootstocks (Carrizo citrange, C-35 citrange and Forner-Alcaide 5) on physicochemical parameters, sugars and organic acids, total antioxidant activity, total phenolic, crude fibre content and flavonoids, of 'Clemenrubí' and 'Orogrós' clementines. The results indicate that the effect of rootstock on the physicochemical parameters, antioxidant activity, total phenolic, sugars and organic acids and flavonoids of clementines fruits is a rather complex phenomenon that greatly depends on specific interactions between the rootstock and each particular scion variety. C-35 citrange rootstock produced the heaviest and bigger size fruits, while the rootstock Forner-Alcaide 5 produced the fruit with the major flavonoid content.