Background: The increasing prevalence of cardiometabolic disease (CMD) in combination with an ageing population is a major public health problem. Early detection and management of individuals at risk for CMD is required to prevent future health problems with associated costs. General practice is the optimal health care setting to accomplish this goal. Prevention programs for identification and treatment of patients with an increased risk for CMD in primary care have been proven feasible. However, the effectiveness and cost-effectiveness have yet to be demonstrated. The 'Personalized Prevention Approach for CardioMetabolic Risk' (PPA CMR) is such a prevention program. The objective of the INTEGRATE study is to investigate the effectiveness and cost-effectiveness of PPA CMR, as well as to establish determinants for participation and compliance. Methods. The INTEGRATE study is designed as a stepped-wedge randomized controlled trial with a waiting list control group. In approximately 40 general practices, all enlisted patients without CMD aged 45-70 years, are invited to participate in PPA CMR. After an online risk estimation, patients with a score above risk threshold are invited to the GP for additional measurements, detailed risk profiling and tailored treatment of risk factors through medication and/or lifestyle counseling. At baseline and after twelve months of follow-up lifestyle, health and work status of all participants are established with online questionnaires. Additionally after twelve months, we will determine health care utilization, costs of PPA CMR and compliance. Primary endpoints are the number of newly detected patients with CMD and changes in individual risk factors between the intervention and waiting list control group. Medical data will be extracted from the GPs' electronic medical records. In order to assess factors related to participation, we will send questionnaires to non-participants and assess characteristics of participating practices. For all participants, additional demographic characteristics will be available through Statistics Netherlands. Discussion. The INTEGRATE study will provide insight into the effectiveness and cost-effectiveness of PPA CMR as well as determinants for participation and compliance, which represents essential information to guide further large-scale implementation of primary prevention programs for CMD. Trial registration number. NTR4277, The Netherlands National Trial Register, 26-11-2013. © 2014 Badenbroek et al.; licensee BioMed Central Ltd.