Highlights: • For all genotypes, drought induces a loss of fruit metabolites content per plant. • This response is modulated through the reduction of the volume of the berries. • Water deficit changes the balance between fruit primary and secondary metabolites. • Sugar concentration is little impacted by water deficit, conversely to malic/tartaric acid ratio. • Anthocyanins/sugars modulation by water deficit is genotype-dependent. Abstract: Adopting disease-tolerant grapevines is an efficient option to implement a smarter management strategy limiting the environmental impacts linked to pesticide use. However, little is known on their production of fruit metabolites regarding expected future climate fluctuations, such as increased water shortage. Moreover, previous studies about how water deficit impacts grape composition, lack accuracy due to imprecise timing of fruit sampling. In this study, we phenotyped six new fungus-tolerant genotypes exposed to varying water status in field-grown conditions. The accumulation of water, main cations, primary and secondary metabolites were precisely monitored at the arrest of phloem unloading in fruits, which was targeted at the whole cluster level. The goal was to decipher the effects of both genotype and water deficit on the allocation of carbon into soluble sugars, organic acids, amino acids and anthocyanins. The results revealed that the effect of decreased water availability was specific to each berry component. While fruit sugar concentration remained relatively unaffected, the malic/tartaric acid balance varied based on differences among genotypes. Despite showing contrasted strategies on carbon allocation into berry metabolites, all genotypes reduced fruit yield and the amount of compounds of interest per plant under water deficit, with the extent of reduction being genotype-dependent and correlated with the response of berry volume to plant water status. This first set of data provides information to help reasoning the adaptation of these varieties according to the expected risks of drought and the possibilities of mitigating them through irrigation. Graphical abstract: https://ars.els-cdn.com/content/image/1-s2.0-S098194282400442X-ga1.jpg