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.