Background: The effects of multidisciplinary treatment programs on eating behavior in overweight preschool-aged children are largely unknown. We evaluated a multidisciplinary intervention program on eating behavior in 3- to 5-year-old overweight children, comparing them with children given standard treatment. We also assessed the parental eating behavior changes and investigated associations between parents and children. Methods: We randomized 75 children to a multidisciplinary intervention or to a standard care program. During a 16-week period, children and parents in the multidisciplinary group were given dietary advice, physical activity sessions and, for parents only, psychological counseling. Children and parents in the standard group visited a pediatrician 3 times and were given information on a healthy lifestyle. At baseline, after 16 weeks, and after 12 months, children were measured and parents completed the Dutch Child Eating Behavior Questionnaire (DEBQ-C) for their children and the DEBQ for themselves. Results: At the three time points, 70 (93.3%), 57 (91.9%), and 42 (73.7%) DEBQ-Cs were analyzed. We found no differences in the changes in eating behavior between the two groups over time. In both groups, there was a significant increase in restrained eating behavior present at 16 weeks, however, this was no longer present at 12 months. We found no associations between changes in eating behavior between the children and their parents. Conclusions: A multidisciplinary obesity intervention program in preschool-aged children induced more restrained eating behavior between baseline and 16 weeks. However, there was no difference with the children in the standard care group.