Abstract Background Improving the lifestyle of overweight and obese adults is of increasing interest in view of its role in several chronic diseases. Interventions aiming at overweight or weight-related chronic diseases suffer from high drop-out rates. It has been suggested that Motivational Interviewing and more frequent and more patient-specific coaching could decrease the drop-out rate. 'BeweegKuur' is a multidisciplinary lifestyle intervention which offers three programmes for overweight persons. The effectiveness and the cost-effectiveness of intensively guided programmes, such as the 'supervised exercise programme' of 'BeweegKuur', for patients with high weight-related health risk, remain to be assessed. Our randomized controlled trial compares the expenses and effects of the 'supervised exercise programme' with those of the less intensively supervised 'start-up exercise programme'. Methods/Design The one-year intervention period involves coaching by a lifestyle advisor, a physiotherapist and a dietician, coordinated by general practitioners (GPs). The participating GP practices have been allocated to the interventions, which differ only in terms of the amount of coaching offered by the physiotherapist. Whereas the 'start-up exercise programme' includes several consultations with physiotherapists to identify barriers hampering independent exercising, the 'supervised exercise programme' includes more sessions with a physiotherapist, involving exercise under supervision. The main goal is transfer to local exercise facilities. The main outcome of the study will be the participants' physical activity at the end of the one-year intervention period and after one year of follow-up. Secondary outcomes are dietary habits, health risk, physical fitness and functional capacity. The economic evaluation will consist of a cost-effectiveness analysis and a cost-utility analysis. The primary outcome measures for the economic evaluation will be the physical activity and the number of quality-adjusted life years. Costs will be assessed from a societal perspective with a time horizon of two years. Additionally, a process evaluation will be used to evaluate the performance of the intervention and the participants' evaluation of the intervention. Discussion This study is expected to provide information regarding the additional costs and effects of the 'supervised exercise programme' in adults with very high weight-related health risk. Trial registration number ISRCTN: ISRCTN46574304