In vegetables, tolerance to drought can be improved by grafting commercial varieties onto drought tolerant rootstocks. Grafting has emerged as a tool that copes with drought stress. In previous results, the A25 pepper rootstock accession showed good tolerance to drought in fruit production terms compared with non-grafted plants and other rootstocks. The aim of this work was to study if short-term exposure to drought in grafted plants using A25 as a rootstock would show tolerance to drought now. To fulfill this objective, some physiological processes involved in roots (rootstock) and leaves (scion) of grafted pepper plants were analyzed. Pepper plants not grafted (A), self-grafted (A/A), and grafted onto a tolerant pepper rootstock A25 (A/A25) were grown under severe water stress induced by PEG addition (-0.55 MPa) or under control conditions for 7 days in hydroponic pure solution. According to our results, water stress severity was alleviated by using the A25 rootstock in grafted plants (A/A25), which indicated that mechanisms stimulated by roots are essential to withstand stress. A/A25 had a bigger root biomass compared with plants A and A/A that resulted in better water absorption, water retention capacity and a sustained CO assimilation rate. Consequently, plants A/A25 had a better carbon balance, supported by greater nitrate reductase activity located mainly in leaves. In the non-grafted and self-grafted plants, the photosynthesis rate lowered due to stomatal closure, which limited transpiration. Consequently, part of NO uptake was reduced in roots. This condition limited water uptake and CO fixation in plants A and A/A under drought stress, and accelerated oxidative damage by producing reactive oxygen species (ROS) and HO, which were highest in their leaves, indicating great sensitivity to drought stress and induced membrane lipid peroxidation. However, drought deleterious effects were slightly marked in plants A compared to A/A. To conclude, the A25 rootstock protects the scion against oxidative stress, which is provoked by drought, and shows better C and N balances that enabled the biomass to be maintained under water stress for short-term exposure, with higher yields in the field.