Background and aims: This study investigated the role of self-regulation competencies in general and specifically in a food-related context for the control of body weight in a three-year weight loss program. Methods: The sample consisted of 30 male and female adolescents (age range: 11–18 years) who participated in a three-year therapy program for severe obesity (mean BMI at the beginning of the intervention was 33.6). Assessment of self-regulation competencies was conducted at three different stages (1st–3rd graduation/class year). Therefore, three independent groups of adolescents (N = 10) at these different stages were tested (initial-to final-stage of therapy). At the time of testing the BMI of these groups significantly differed from 38.8 to 28.7. Analyses of covariance were performed to determine whether the adolescents also differed in self-regulation skills like “resistance to temptation” and food-related Stroop interference along with ameliorating their energy-balance regulation. Results: In addition to the main effects of age and body mass index, adolescents further displayed significant improvements of executive functions with respect to resistance to temptation and inhibition. Conclusions: Interventions aimed at enhancing energy-balance regulation in adolescents may further benefit from efforts to facilitate executive functions such as self-regulation and food-related cognitive inhibition.