<p>Case numbers of metabolic diseases such as diabetes and hyperlipidaemia are increasing worldwide and show geographic heterogeneity, but the role of environmental geography in shaping this pattern is poorly defined. Here we integrate large multi-region cohorts in China (<i>n</i> = 3,648 cross-sectional; <i>n</i> = 1,547 prospective) with high-resolution soil trace-element data to test whether geography shapes levels of dietary ions and risk of metabolic disease. We observe geographic variations in levels of serum and urinary trace elements, with selenium, zinc and chromium linked to metabolic outcomes. Soil selenium was a predictor of serum selenium in participants even after incorporating regional dietary, socioeconomic and air-quality indicators. In a prospective cohort, participants in the highest serum selenium tertile (107.2–162.8 µg l⁻¹) had a 35% higher risk of incident diabetes than those in the lowest tertile (relative risk (RR) = 1.35; 95% confidence interval (CI) = 1.02–1.77) after multivariable and dietary adjustment; the association was significant in men (RR = 1.96; 95% CI = 1.21–3.17), but not in women (RR = 1.10; 95% CI = 0.77–1.58). Globally, an estimated 14% of land area—home to approximately 1 billion people—has high soil selenium, with residents projected to have serum selenium levels above 110 µg l⁻¹, a range in which selenium supplementation could increase diabetes risk.</p>