Owing to high nutritional value and improved bioavailability of essential elements, microgreens are promising targets for nutrient enrichment using technological aspects of light-emitting diodes. This study determines changes in metabolism of certain prebiotic carbohydrate (hexoses and sucrose), ascorbic acid, β-carotene; nonheme iron (Fe) enrichment and interaction with inorganic catalysts, such as magnesium (Mg) or calcium (Ca) in Brassicaceae (kohlrabi Brassica oleracea var. gongylodes, broccoli Brassica oleracea and mizuna Brassica rapa var. Japonica) microgreens. Plants grew under main LED lighting spectrum (combination of blue 447 nm, red 638 and 665 nm and far-red 731 nm) or supplemented with green 520 nm, yellow 595 nm and orange 622 nm LEDs. Photoperiod of 16 h and total PPFD of 300 µmol m-2 s-1 was maintained. Obtained results highlight the impact of supplemental LED components and provides key information to improve microgreens nutritional quality. Supplemental 595 nm significantly increased content of prebiotic carbohydrates in mizuna and broccoli. Significantly positive effect of supplemental components on β-carotene accumulation was observed only in mizuna, whereas kohlrabi distinguished in significant accumulation of ascorbic acid. Supplemental 622 nm component led to a significant increase of Fe, Mg and Ca in all microgreens. Generally, the accumulation of Fe was highly dependent on promoters and inhibitors of Fe absorption, as very strong positive correlation between Fe and Ca, Fe and Mg was found in kohlrabi and broccoli, whereas, strong negative correlation between Fe and β-carotene, Fe and prebiotic carbohydrates was found only in kohlrabi. Thus, metabolic changes that occurred in treated microgreens increased the bioavailability of essential nutrients. Therefore, selected supplemental LEDs, might be a preferred option for Brassicaceae microgreens cultivation to preserve and accumulate certain nutritionally valuable metabolites.