There is a general belief that having breakfast is an important healthy lifestyle factor; however, there is scarce evidence on the influence of breakfast quality and energy density on cardiometabolic risk in children, as well as on the role of physical activity in this association. The aims of this paper were (i) to examine the associations of breakfast quality and energy density from both solids and beverages with cardiometabolic risk factors, and (ii) to explore whether physical activity levels may attenuate these relationships in children with overweight/obesity from two projects carried out in the north and south of Spain. Breakfast consumption, breakfast quality index (BQI) score, BEDs/BEDb (24 h-recalls and the KIDMED questionnaire), and physical activity (PA; accelerometry) were assessed, in 203 children aged 8-12 years who were overweight or obese. We measured body composition (Dual X-ray Absorptiometry), uric acid, blood pressure, lipid profile, gamma-glutamyl-transferase (GGT), glucose, and insulin, and calculated the HOMA and metabolic syndrome z-score. The BQI score was inversely associated with serum uric acid independently of a set of relevant confounders ( = -0.172, p = 0.028), but the relationship was attenuated after further controlling for total PA (p < 0.07). BEDs was positively associated with total and HDL cholesterol, and systolic blood pressure regardless of confounders (all p < 0.05), while BEDb was positively associated with HOMA in either active/inactive children (all p < 0.03). In conclusion, higher breakfast quality and lower breakfast energy density should be promoted in overweight/obesity children to improve their cardiometabolic health.