Despite phenotypic plasticity that allows the adaptation to harsh environments, when vines experience severe abiotic stresses, they can suffer from metabolic damages affecting grape production and quality. Grafting is an affordable strategy to mitigate these negative consequences since the rootstock can increase the drought tolerance in the scion. This work explored the effects of pre-veraison water deficit on vines grafted on different rootstocks (Mgt 101-14 and 1103 Paulsen) to obtain physiological, biochemical, and molecular information about the influence on grape quality. Repeated measurements were carried out to assess vine physiology, production, technological maturity, and berry phenolic composition. qRT-PCRs were executed on berry skins at maturity to assess the expression levels of ten genes and five miRNAs involved in the phenylpropanoid pathway. Water stress caused significant alterations in grape technological maturity. The rootstock effect was not detected in primary metabolism while it was well defined in the accumulation of phenolic compounds in berries (such as anthocyanins). Finally, significant differences were identified in gene and miRNA expression between water-stressed and well-watered vines. In conclusion, the response to water stress can be modulated by rootstocks, which mainly act by regulating secondary metabolism, especially in grapes.