As in adults, childhood obesity is associated with several metabolic disorders; however, there is little information regarding complex obesity-derived complications such as hepatic steatosis or endothelial dysfunction at early ages. Therefore, the objective of the present study was to analyze the effect of a nutritional and physical exercise program on obesity comorbidities in the form of subclinical atherosclerosis and non-alcoholic fatty liver in young children. A total of 148 children completed the study. For nine months (one academic year), children carried out a nutritional and physical activity program of 3 h/week. Anthropometric, clinical, liver ultrasound and carotid intima-media thickness (cIMT) parameters were evaluated. Our results showed that the program significantly improved anthropometrical parameters, especially regarding BMI and body fat ( < 0.001 and = 0.004, respectively). The effect on metabolic parameters was limited, although a significant reduction on triglycerides was observed ( = 0.009). The education program had a great influence on the echogenic parameters, since the percentage of children with light steatosis decreased from 35% to 4% at the end of the study. In addition, cIMT also decreased significantly in both groups, although there was no statistically significant differences between groups. In conclusion, detection of early complications of obesity through sonographic parameters may allow early intervention, as in the present study, to prevent obesity co-morbidities in children.