Obesity is a worldwide epidemic with a high prevalence of comorbidities, including alterations in bone mineral metabolism. The purpose of this yearlong study was to evaluate the role of 2 types of exercise training (aerobic and aerobic plus resistance exercise) on adipokines parameters and bone metabolism in adolescents who are obese. This was a clinical trial study with interdisciplinary weight loss therapy. Forty-two postpubertal adolescents who are obese were subjected to interdisciplinary weight loss therapy with physical exercise, medical monitoring, nutritional intervention, and psychological intervention. Data were collected from serum analyses of leptin, ghrelin, adiponectin, glucose, and insulin. Anthropometric measurements of body composition, bone mineral density, visceral, and subcutaneous fat were also performed. Statistical tests were applied using repeated-measures analysis of variance. Correlations were established using the Pearson test, and dependencies of variables were established using simple linear regression test. Both training types promoted reductions in body mass index, total central, visceral and subcutaneous fat, insulin concentration, and homeostasis model assessment insulin resistance (HOMA-IR) index, but only aerobic plus resistance training showed statistical improvements in the bone mineral content, adiponectin concentration, and lean tissue. Effective reduction in the visceral/subcutaneous ratio, central/peripheral ratio, and leptin concentration was observed. Insulin and the HOMA-IR index were negative predictors of bone mineral content in the combined training group. Moreover, fat distribution was a negative predictor for bone mineral density in both groups. Aerobic plus resistance training promotes a protective role in bone mineral content associated with an improvement in adiponectin and leptin concentrations, favoring the control of the inflammatory state related to obesity in adolescents. Aerobic plus resistance training combined with interdisciplinary interventions provides important strategies to approach obesity, and these strategies may contribute to clinical practice.