Pomegranate trees are known for their ability to withstand drought conditions, but there is still much to learn about how water stress affects the lipobiochemical behavior of their seeds. This study aimed to investigate how sustained deficit irrigation (SDI-50), equivalent to 50% of crop evapotranspiration, influences pomegranate seed oil attributes such as phenols, flavonoids, and tannins content, and the seeds’ lipochemical fingerprints compared to fully irrigated trees. At the full ripening stage, pomegranate seeds were analyzed for their oil content, biochemical traits, and vibrational fingerprints using infrared radiation. The results indicated that there was a significant genotypic effect coupled with applied water stress on all the investigated traits. Interestingly, an increasing trend in seed oil yield was observed under water stress conditions compared to the control, with the highest oil yield increase observed in the ‘Zheri Precoce’ fruit seeds. Only two cultivars did not show the same pattern, with the oil yield increase ranging from 8% to 100%. Furthermore, SDI-50 induced a substantial increase in total phenolic content, coupled with a significant genotypic effect, and resulted in an average increase of 7.5%. This increase in total phenolics also correlated with an increase in antioxidant activity across all investigated cultivars. ATR-FTIR fingerprinting revealed eleven spectral fingerprints corresponding to functional groups present in pomegranate seeds oil, with a particular pattern of significant effects of both genotypic and SDI-50 factors. These results suggest that exploiting water scarcity conditions could be a viable approach to improve the quantitative and qualitative attributes of pomegranate seed oil. While there are still several aspects to be investigated further, this study provides a basis for pomegranate processing under water shortage conditions.