Abstract Background Alcohol use disorder is a widespread problem in Denmark and has severe impacts on health and quality of life of each individual. The clinical treatment of alcohol use disorder involves evidence-based knowledge on medical treatment, physical training, and psychological management. The aim of this study is to investigate the effect of physical exercise on alcohol intake, cardio-respiratory fitness and socio-psychological outcomes. Methods/design The study is a randomized controlled trial with three arms: (A) Standard treatment alone, (B) Standard treatment and physical exercise in groups, or (C) Standard treatment and physical exercise on an individual basis. The patients will fill a questionnaire and they will be tested at baseline, and after 6 and 12 months. Discussion If this study detects a positive relationship between exercise as a supplement to alcohol treatment and patients’ alcohol intake, quality of life, fitness, well-being, anxiety, depression and interpersonal problems, it will be recommended to implement exercise as an offer to users of the outpatient clinic in the future. Trial registration Current Controlled Trials ISRCTN74889852 .