The present study involved the bio-fabrication of silver nanoparticles (AgNPs) by using the Euphorbia helioscopia L. leaves aqueous extract to improve the production of secondary metabolites in industrially important sunflower (Helianthus annuus L.) plants. Phyto-fabrication of AgNPs was confirmed by using spectrophotometry, SEM imaging and X-ray diffraction analysis. The morphological and optical characterization manifested that the AgNPs are crystalline and exist in the size range of 30–100 nm. Various concentrations (10, 20, 40, 60, 80 and 100 mg/L) of AgNPs were applied in combinations on sunflower seeds and crop plants. The effects of biosynthesized AgNPs were evaluated for agro-morphological parameters (plant height, flowering initiation and seed weight), biochemical metabolites (chlorophyll, proline, soluble sugar, amino acid and protein contents) and enzymatic activities (superoxide dismutase and ascorbate peroxidase) in sunflower and 60 mg/L concentration of AgNPs on sunflower seeds and foliar sprays on plants in combination were found to be effective to elicit biochemical modifications to improve secondary metabolites. It was also observed experimentally that 60 mg/L concentration of AgNPs improved the biochemical, fatty acid and enzymatic attributes of sunflower plants, which in turn improved the plant agro-morphological parameters. Near-infrared spectroscopic analysis results confirmed the improvement in the seed quality, oil contents and fatty acid composition (palmitic acid, oleic acid and linoleic acid) after the applications of AgNPs. The findings of the present investigation confirm the exogenous applications of bio-fabricated AgNPs in combinations on seeds and plants to improve the plant yield, seed quality and secondary metabolite contents of the sunflower plants.