Environmental and anthropogenic activities are pushing the earth towards warmer years, which is reducing agricultural land and causing water scarcity. It is well documented that sunflower (being drought tolerant) crops can be grown under water deficit conditions with some additional supportive priming applications to compensate for drought-induced challenges. However, finding the most efficient and eco-friendly priming tools is always a top priority among researchers to improve plant growth, adaptive traits, and productivity. In this study, an experiment was performed on oil-producing crops (sunflower) using seed magnetic treatment. The seeds were subjected to 0.1, 0.2, and 0.3 Tesla for 20 min, respectively. Plants were exposed to water limitation (100 and 50%) after 30 days of germination. Sunflower showed its tolerance to water limitation by maintaining the majority of growth parameters, nutritive value, metabolizable energy, and higher proline content. Nevertheless, a reduction in the achene number per capitulum, capitulum weight, chlorophyll, catalase activity, unsaturated to saturated fatty acids, anthocyanin, and hydroxyl derivatives of cinnamic acid supported our hypothesis about the need for some supportive techniques. Better metabolic adjustment and percentage of oil yield were manifested by 0.3 T magnetic seed treatment, which was used for phenolic and fatty acid profiling. To conclude, magnetic treatment of seeds may improve their primary metabolic capacity and antioxidation potential, which in turn may activate their secondary metabolism as evidenced by an excess of gallic acid, quercetin, benzoic acid, curcumin acid, sinapic acid, and chlorogenic acid.