Aerobics or strength exercise plus diet interventions have been shown to counteract childhood obesity. However, little is known with regard to periodized multicomponent exercise interventions combined with nutritional counselling, which might be less demanding but more enjoyable and respectful of children and adolescents’ nature. In order to analyze the impact of such a multimodal approach, 18 obese children (10.8 ± 1.6 years; 63% females; z Body Mass Index 3 ± 0.4) trained for 60 min, twice weekly and were measured for body composition, biochemical parameters and physical function. We found that 16 weeks of multimodal intervention (14 of training), based on fun-type skill-learning physical activities and physical conditioning with challenging circuits and games, together with nutritional counselling, led to an attendance > 80%, with significant overall health improvement. Body composition was enhanced (p < 0.01 for z BMI, mid-upper-arm-circumference, waist-to-height ratio, tricipital and subscapular skinfolds, body-fat % by Slaughter equation and Dual energy X-ray absorptiometry body fat% and trunk fat%), as well as metabolic profile (LDL cholesterol, gamma-glutamyl transferase , alanine aminotransferase ; p < 0.05), homeostatic model assessment of insulin resistance (HOMA-IR; p < 0.05) and inflammatory response (C-Reactive Protein; p < 0.05). Physical fitness was also improved (p < 0.01) through better cardiovascular test scores and fundamental movement patterns (Functional Movement Screen-7, FMS-4). Tailoring multimodal supervised strategies ensured attendance, active participation and enjoyment, compensating for the lack of strict caloric restrictions and the low volume and training frequency compared to the exercise prescription guidelines for obesity. Nutritional counselling reinforced exercise benefits and turned the intervention into a powerful educational strategy. Teamwork and professionals’ specificity may also be key factors.