The purpose of the research was to study the effect of the quercetin-Ferrum complex on the synthesis of plastid pigments and secondary metabolites in berry crops. In the research, biotechnological, physiological, biochemical and statistical methods were used. The ability of quercetin, which is one of the most common flavonol aglycons, to create a chelated complex with Fe2+ and regulate physiological processes associated with oxidation-reduction reactions, synthesis of pigments and metal enzymes when being a supplement of nutrient medium is shown. With the addition of quercetin-Ferrum complex with a fraction of Fe2+ in a concentration equivalent to the base nutrient media composition optimized for the cultivation of berry crops in vitro, regenerated plants showed a sufficiently high regeneration capacity. Based on the indicators of the content of chlorophylls and carotenoids in leaves, the physiological availability of Ferrum in the quercetin-Ferrum complex was established. The concentration of chlorophylls a and b in raspberry and strawberry leaves increased by 20−25%, and the content of carotenoids increased by 30−40%. On the contrary, in black currant, the content of chlorophyll a in leaves decreased by 18−20% and chlorophyll b by almost 75%. It was found that quercetin is a biologically active phenolic chelating agent capable of chemically binding Fe2+ ions and participating in the regulation of growth processes, in particular in the induction of callusogenesis. Metal-flavonol complex is advisable to use in micro clonal reproduction of plants sensitive to oxidative stress in conditions of Fe2+ ions deficiency under the condition of individual selection of the components of the chelate complex and adjusting its concentration in the nutrient medium.