In the current study, the effects of drought stress on the growth and phytochemical profile of Scolymus hispanicus L. (a.k.a. golden thistle) were evaluated. Plants were treated with three irrigation regimes, e.g., plants that received only rainwater (Control; C), deficit irrigation (I1; 50% of field capacity (FC)), and full irrigation (Ι2; 100% of FC). The fresh weight of the rosette of leaves was not negatively impacted by deficit irrigation, whereas root development was severely restrained compared to control and I2 treatments. Drought stress conditions had a positive effect on the nutritional properties of the golden thistle since the treatments of control and deficit irrigation showed the highest content of macronutrients and energy. Oxalic acid was the richest organic acid, especially under the I1 regime. Similarly, α-tocopherol was the only identified vitamin E isoform, whose content was also doubled in I1 treatment. Raffinose, glucose, and sucrose were the most abundant free sugars in amounts that varied among the irrigation treatments, while the total and distinct free sugar content was the highest for the I1 treatment. The most abundant detected fatty acid compounds were α-linolenic acid, followed by palmitic and linoleic acid, with the highest amount being detected in C, I1, and I2 treatments, respectively. Flavonoids were the only class of polyphenols detected in golden thistle leaves, including mostly kaempferol and quercetin derivatives. The greatest antioxidant potency was shown for the control and I1 treatments (for OxHLIA and TBARS methods, respectively). The evaluated leaf samples recorded a varied antimicrobial effect for the different bacterial strains and fungi, whereas no cytotoxic, hepatotoxic, and anti-inflammatory effects against the tested cell lines were recorded. Finally, the mineral content of leaves was significantly affected by the irrigation regime, with Ca, Mg, Cu, and Zn being the highest for the I1 treatment, while the I2 treatment had the highest content of K, Fe, and Mn and the lowest Na content. In conclusion, deficit irrigation showed promising results since it improved the phytochemical content without compromising the fresh weight of leaves, and thus it could be suggested as a sustainable agronomic practice for producing high-added value products without significant constraints in growth development and yield parameters of golden thistle.