Childhood obesity results in premature atherosclerosis and requires early intervention. Compare the effectiveness of 6-month lifestyle interventions (with choice of either individual or group therapy) with standard care on body mass index (BMI) z-score and cardiovascular disease (CVD) risks factors in children with obesity. This 6-month randomized controlled trial with a 6-month follow-up included 74 pre-pubertal children with obesity (7.5-11.9 years) assigned randomly (2:1) to intervention or control. Families in the intervention arm choose between an individually delivered treatment (3 hours paediatrician + 4 hours dietician) or group treatment (35 hours with a multidisciplinary team). Children participated also to a weekly physical activity programme. We measured BMI, BMI z-score; waist circumference (WC); total and abdominal fat; blood pressure; common carotid artery intima-media thickness and incremental elastic modulus (Einc); endothelium-dependent and independent dilation (nitroglycerin-mediated dilation [NTGMD]) of the brachial artery; fasting plasma glucose, insulin, lipids; and high-sensitivity C-reactive protein (hs-CRP). Compared to controls, at 6 months, abdominal fat and hs-CRP were reduced in both interventions. The group intervention was also effective in reducing BMI (-0.55 kg/m2 ; 95% confidence interval -1.16 to 0.06) and BMI z-score (-0.08; -0.15 to 0.00) at 6 months and BMI, BMI z-score, WC, NTGMD, total and abdominal fat at 12 months. Abdominal fat and low-grade inflammation were significantly decreased in both interventions. High-intensity group treatment improved early signs of atherosclerosis in children with obesity. These findings are important for the promotion of cardiometabolic health in this population.