Calcium intake has been associated with lower adiposity, but few studies explored the longitudinal relation of calcium from different sources and cardiometabolic markers in young population. Prospectively estimate the association between dairy and non-dairy calcium intake at 4, 7, and 10 years (y) of age and cardiometabolic risk at 13 y. The sample included 4017 participants from the Generation XXI birth cohort. Dietary data were collected from a 3-day food diary. Cardiometabolic clusters at 13 y were estimated by a probabilistic Gaussian mixture model (z-score of waist circumference [WC], HOMA-IR; HDL cholesterol, triglycerides, and systolic blood pressure [BP]). Multivariable linear and logistic regression models were used to estimate associations. Calcium intake (/100 mg), after adjustment for confounders, was negatively and significantly associated with body mass index (BMI) (β = -0.02, 95% CI: -0.04; -0.01), WC (cm) (β = -0.23, 95% CI: -0.36; -0.11), and diastolic BP (mmHg) (β = -0.14, 95% CI: -0.26; -0.03). After additional adjustment for total energy intake, associations lose statistical significance. Calcium intake from milk at 7 y was inversely associated with WC (β = -0.25, 95% CI: -0.48; -0.03) and from yogurt at 10 y was associated with higher BMI (β = 0.08, 95% CI: 0.03; 0.13) and WC (β = 0.54, 95% CI: 0.12; 0.96). Calcium from vegetables at 4, 7, 10 y reduces later cardiometabolic risk (OR = 0.71; OR = 0.84; OR = 0.98, respectively). This study supports a protective effect of calcium on adolescents' cardiometabolic health, especially from vegetables.