Purpose Diet is an important determinant of cardiometabolic disease risk in adults. We aimed to study associations of diet quality with cardiometabolic health in school-age children. Methods This study was embedded in the Generation R Study a prospective population-based cohort in Rotterdam, the Netherlands and included 3991 children. Food intake was assessed with a Food-Frequency Questionnaire at age 8 years. A diet quality score (0–10) was calculated reflecting adherence to age-specific dietary guidelines. The following outcome variables were measured at age 10 years and used to create a continuous cardiometabolic risk factor score: body fat percentage, insulin, triglycerides, HDL cholesterol, and systolic and diastolic blood pressure. Outcomes were expressed in age- and sex-specific standard deviation scores (SDS). Multivariable linear regression models were used to assess associations between the diet quality score and the cardiometabolic risk factor score and with the individual cardiometabolic risk factors. Results In models adjusted for socioeconomic and lifestyle factors and BMI, a higher diet quality was associated with a lower cardiometabolic risk factor score [− 0.08 per point higher diet score, (95% CI − 0.15, − 0.001)]. This association was mainly driven by associations of higher diet quality with lower systolic [− 0.04 SD (95% CI − 0.06, − 0.01)] and diastolic blood pressure [− 0.05 SD, (95% CI − 0.07, − 0.02)]. No statistically significant associations were found for insulin, triglycerides, HDL cholesterol, or body fat percentage as individual factors. Conclusions We found an association between higher diet quality and better cardiometabolic health in childhood, mainly driven by a lower blood pressure. Further research is needed to explore associations of diet quality in childhood with long-term cardiometabolic health.