<p>This research studied the impact of bare iron oxide nanoparticles (Fe₃O₄ NPs), citrate-stabilized iron oxide nanoparticles (Fe₃O₄CA NPs), and indole-3-acetic acid (IAA) on the genetic stability and metabolic activity of <i>Chrysanthemum × morifolium</i> (Ramat.) Hemsl. plants obtained from synthetic seeds. For this purpose, axillary buds of chrysanthemum ‘Richmond’ were embedded in 3% calcium alginate supplemented with NPs and IAA, either singularly or in combination. Next, the synthetic seeds were stored at 4&#xa0;°C in the dark (for eight weeks) on an agar-water medium and then transferred to room temperature for 30 or 60 days. Next, the germinated seeds were transplanted to the greenhouse until the plants were fully flowering. The total polyphenol content (TPC) was determined in the leaves and inflorescences of the plants. Moreover, the content of anthocyanins was measured in the inflorescences. RAPD markers were used to assess the genetic stability of plants. Most treatments stimulated the accumulation of polyphenols in the leaves of chrysanthemum by as much as 59% after 30 days, and up to 28% after 60 days. Fe₃O₄NPs and IAA + Fe₃O₄CA NPs stimulated the biosynthesis of polyphenols and anthocyanins in the inflorescences after 30 days of treatment (by 36% and 68%, respectively); however, a decline in the content of these compounds (22–33%) was reported after 60 days in most experimental objects, except for Fe₃O₄CA NPs and IAA + Fe₃O₄CA NPs. The inflorescences of plants treated with nanoparticles usually exhibited a larger diameter than the control, but only after a shorter exposure to the analyzed factors. In contrast, prolonged treatment resulted in an opposite effect. The genetic uniformity of the plants was confirmed as no polymorphism was detected in 2160 RAPD markers.</p>