Iron and zinc deficiencies in semi-arid regions limit crop productivity and contribute to global malnutrition. To address these challenges, a split-plot factorial design was employed over two growing seasons (2019-2021). This study evaluated the effects of fertilizers, including bulk and nanoparticle (NPs) forms of Fe (Fe2O3) (1-100, 20-30, 50-60, and 80-100 nm), as well as Zn (ZnO) (1-100, 10-30, 40-60, and 80-100 nm) at three concentrations: 0, 300, and 600 mg L- 1 in well-watered (WW) and late-season water deficit (WD) environments on Flaxseed. In WW, the average yields of seeds, protein, oil, and mucilage were 2028, 464, 583, and 99 kg ha- 1, respectively, and WD significantly reduced them. In WD, fertilizers, compared to nonfertilizer treatment, significantly increased the above traits. Fe-NPs 20-30 nm 600 mg L- 1 and Zn-NPs 40-60 nm 300 mg L- 1 produced the highest oil percentage in WW (35.25 %) and WD (29.38 %), respectively. WD and fertilizers significantly decreased linolenic and stearic acid and increased oleic and linoleic acid. In WW, Fe-NPs 20-30 nm 600 mg L- 1 (29.9 %). NP fertilizers outperform bulk fertilizers, improving seed quality, mitigating WD effects, and boosting Flaxseed production. They address global micronutrient deficiencies, offering a resilient agricultural solution and enhancing nutritional security worldwide.