BACKGROUND: Magnesium (Mg) fertilization is a promising practice to improve vegetable yield. However, its impacts on vegetable quality and human health have not been examined. Thus, a field experiment was conducted to investigate the effects of varying Mg fertilization rates on yield and quality of pepper (Capsicum annuum L.) fruit. Furthermore, result of the field experiment was linked to pepper consumption data from the China Health and Nutrition Survey (CHNS) in the disability-adjusted life years (DALYs) framework to evaluate the potential health impact of Mg fertilization for the first time. RESULTS: Compared to control, Mg fertilization increased the 2-year average pepper yield by 25.6%, whereas there was no significant yield improvement when Mg rates exceeded 112.5 kg MgO ha −1. Magnesium application increased concentrations of Mg and capsaicinoids, decreased those of calcium (Ca), zinc (Zn) and vitamin C (Vc), and had no effect on potassium (K) and iron (Fe) in pepper fruit. As a result, Mg fertilization decreased the comprehensive nutrition level of pepper by 16.6%. Furthermore, the current health burden of the Chinese adult population associated with pepper consumption is estimated at 21.3 million DALYs per year, with the risk being increased by 5.40 DALYs for per megagram of Mg fertilizer application. Increasing health risk was mainly attributed to decreasing concentrations of Ca and Vc in pepper fruit, though the increased Mg intakes offset the impact of 1.74% to 14.4%. CONCLUSION: Magnesium fertilization significantly improved the yield but reduced nutritional quality of pepper fruit, and increased human health risks associated with consumption of pepper fruit.