The purpose was to examine the cross-sectional associations of stress-related reports and stress biomarkers with metabolic syndrome (MetS) risk in children while also testing the interaction between stress biomarkers and stress reports. In 353 children (5-10 years old, 7.9% overweight/obese), MetS risk was measured by blood pressure, waist circumference, glucose homeostasis, triglycerides, and high-density cholesterol. Stress was measured by stress-related reports (events, emotions, and internalizing/externalizing problems) and two biomarkers: salivary cortisol (total-day and morning output) and heart rate variability (percentage of consecutive normal RR intervals differing more than 50 ms and low-to-high-frequency ratio). Cross-sectional regression analyses with z scored total MetS risk as outcome were adjusted for age, sex, and socio-economic status. Only internalizing problems were directly related to a higher MetS risk score (β = 0.236). Cortisol and heart rate variability were significant moderators: High cortisol morning output resulted in a positive (unfavourable) report-MetS relationship (β = 0.259-0.552), whereas low percentage of consecutive normal RR intervals differing more than 50 ms resulted in a negative (favourable) report-MetS relationship (β = -0.298) and low low-to-high-frequency ratio in a positive (unfavourable) report-MetS relationship (β = 0.478). In conclusion, stress can sometimes be a disadvantageous factor in metabolic health of otherwise healthy children. The cortisol biomarker seems relevant because metabolic risk was highest when stress-related reports were accompanied by high morning cortisol output.