Deficit irrigation (DI) strategies are becoming increasingly common in areas where water resources are limited. The application of moderate levels of DI can result in water savings with a small reduction in yield but with a higher quality of the product. The aim of this work was to evaluate the effect of applying a certain level of water deficit (40% water holding capacity) on the yield and quality of the common bean (Phaseolus vulgaris L.), specifically the cultivar ‘Triunfo-70’. Bioactive compounds were investigated by applying an LC-MS-based untargeted metabolomics approach as an analytical tool for identifying novel markers associated with a water deficit in beans. The results showed that beans harvested 30 days after DI application experienced water stress, as indicated by the decrease in the leaf water potential and gas exchange values (stomatal conductance and photosynthesis). In addition, the number of pods per plant was significantly reduced by the DI treatment. The water deficit induced significant alterations in various bioactive compounds (including organic acids, polyphenols, hydroxybenzoic acids, lipids, and phospholipids) when compared to the control treatment. Additionally, twelve new biomarkers were identified in this study for the first time in the common bean under DI. These findings suggested that DI acted as an elicitor, increasing phenylpropanoid metabolism, while concurrently reducing the production of compounds associated with fatty acid metabolism. Additionally, new metabolites were tentatively identified in common beans. This study represents the successful application of the untargeted metabolomics approach to finding bioactive secondary metabolites in beans under different irrigation conditions.