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Analyzing the effects of interventions from a theoretical and statistical perspective that allows understanding these dynamic relationships of obesity etiology can be a more efficient and innovative way of understanding the phenomenon's complexity. Thus, we aimed to analyze the pattern of cardiovascular risk factors between-participants, and the effects within-participants of a multidisciplinary intervention on cardiovascular risk factors in overweight children. This is a randomized clinical trial, and 41 participated in this study. A multicomponent intervention (physical activities, nutritional and psychological counseling) was performed for 10 weeks. Anthropometric and hemodynamics measurements, lipid and glucose profile, cardiorespiratory fitness, and left ventricular mass were evaluated. A network analysis was done. Considering patterns in the network at baseline, WC, WHR, BMI, and Fat were the main variables for cardiovascular risks. Group was the most critical variable in the within-participant network. Participating in a multicomponent intervention and decreasing body fat promoted beneficial cardiovascular factors.