Increased anthropogenic activities have led to the accumulation of certain minerals to ecotoxic levels in the environment, which could influence the secondary metabolism of plants. Shikonin, an exudate from the roots of Onosma dichroantha, is a secondary metabolite involved in plant defense and invasion success; however, the interactive effects of copper (Cu), cadmium (Cd), calcium (Ca), and nitrate (NO3) in shikonin biosynthesis and accumulation are not known. Here, the individual, curvilinear, and pairwise effects of these elements on shikonin biosynthesis in callus culture of O. dichroantha have been investigated by means of a statistical modeling approach and multivariate regression analyses. Although the main effects of the examined minerals seemed to be suppressive, their combined interactions could enhance callus growth and secondary metabolism of O. dichroantha. Accordingly, maximum values were recorded for the callus growth index (6.85 at 23.25μM Cu, 70mM NO3, 1mM Ca, 27.50μM Cd), total phenolics (24.83mg gallic acid equivalent at 9.75μM Cu, 70mM NO3, 1mM Ca, 62.50μM Cd), total flavonoids (6.12mg quercetin equivalent at 30μM Cu, 80mM NO3, 1.5mM Ca, 45μM Cd), and shikonin (24.33μgg-1 FW at 9.75μM Cu, 70mM NO3, 2mM Ca, 27.5μM Cd). Overall, these data show that increasing concentrations of the examined minerals in culture medium can markedly influence the secondary metabolism of O. dichroantha cells and suggest that a comparable phenomenon may exist in a wider range of medicinal plants, grown on polluted environments, which may affect their invasive capabilities.