The main effects of three different irrigation regimes, i.e., sustained deficit irrigation (SDI), regulated deficit irrigation (RDI) and non-irrigated (NI), on seed traits namely proanthocyanidins (PAs) were evaluated in the wine grape cultivar Aragonez (syn. Tempranillo) grown in Alentejo (Portugal) over two growing seasons. Results showed that while the number of seeds per berry was not affected by water availability, seed fresh weight differed among treatments, the NI treatment exhibiting the lowest values. The biosynthetic pathway of flavanols appeared to be modified by the irrigation treatment, and several genes responsible for PA synthesis were up-regulated in the most stressed seeds (RDI and NI). However, this effect had no impact on PA content, suggesting the influence of other factors such as oxidation and/or degradation of PAs at late stages of maturation in grape seeds. The seeds' non-enzymatic antioxidant capacities (oxygen radical absorbance capacity (ORAC) and hydroxyl radical adverting capacity (HORAC)) were modulated by water deficit and correlated well with PA content. The impact of irrigation strategy on PA biosynthesis, content, and anti-radical activity during seed ripening is discussed in the context of increasing interest in the role of PAs in the color and taste of wine, and the potential health benefits relating to their antioxidant capacity.