This study investigates the impact of nitrogen (N), sulfur (S), and iron (Fe) fertilization on secondary metabolites, particularly quercetin and its forms, in onion bulbs (Allium cepa L.). Field experiments over two years examined four onion varieties with red, yellow, and white colors of bulbs: Kamal, Robin, Pueblo, and Mundo. The parameters investigated included the yield, dry matter content, and average onion weight. The phenolic and flavonoid contents were also analyzed. The free quercetin, bound quercetin, and total quercetin contents were determined using the HPLC method. The results demonstrated notable increases in yield following the application of nitrogen (NH4+) and sulfur (SO42−) fertilizers. Incorporating iron (Fe2+) alongside these fertilizers did not yield a significant impact compared to N+S variant. The phenolic and flavonoid content varied with fertilization, while the quercetin content did not yield statistically significant results. Overall, the study highlights the complex relationship between fertilization practices and secondary metabolite production in onions, emphasizing the need for sustainable intensification in modern agriculture.