Pharmaceutical, food and cosmetic industries have shown great interest in grape seed extract due to its premium antioxidant activity with protective effects on human health. However, global climate change has already negatively affected the biochemistry and functionality of such nutraceutical crops. The present study was conducted to reveal the effects of sustained deficit irrigation on certain features of seed extracts obtained from the grape cultivar ‘Prima’ grafted on six genetically different rootstocks during two consecutive years. In both years, seed weight of ‘Prima’ grapes grafted on 5 BB significantly decreased in response to water treatments, although the other rootstocks did not impair the seed weight, except for 44–53 M in 217. Significant decreases in antioxidant activity of the scion cultivar occurred in response to DI when grafted on 5 BB in both years and in 44–53 M in 2017. However, the use of 99 R, 110 R and 140 Ru did not markedly impair the seed antioxidant activity in response to DI condition in both years. In both years, seed anthocyanins of FI vines were always higher than those of DI vines. In 2017, there were significant decreases in anthocyanins due to DI in vines grafted on 5 BB, 44–53 M, 99 R and 110 R. These rootstocks also led significant decreases in anthocyanins of the second year, while the use of 140 Ru and 1613 C rootstocks did not lead significant changes in anthocyanins in both two years. In 2017, total phenolics increased in response to DI, except for the vines grafted on 44–53 M. Rootstock-dependent changes in total phenolics in response to irrigation treatments were insignificant for the vines grafted on 5 BB and 44–53 M in both two experimental years. Averaged data showed that antioxidant activity showed significantly positive correlation with anthocyanins and total phenols. The findings are anticipated to guide future projects on enhancement of the quality and quantity of precious seconder metabolites with sustainable precision viticulture techniques to match the globally increasing demands on bioactive compounds.