Background: Large gaps exist in the implementation of guideline recommendations for cardiovascular disease (CVD) risk management. Electronic decision support (EDS) systems are promising interventions to close these gaps but few have undergone clinical trial evaluation in Australia. We have developed HealthTracker, a multifaceted EDS and quality improvement intervention to improve the management of CVD risk. Methods/design: It is hypothesised that the use of HealthTracker over a 12-month period will result in: (1) an increased proportion of patients receiving guideline-indicated measurements of CVD risk factors and (2) an increased proportion of patients at high risk will receive guideline-indicated prescriptions for lowering their CVD risk. Sixty health services (40 general practices and 20 Aboriginal Community Controlled Health Services (ACCHSs) will be randomised in a 1:1 allocation to receive either the intervention package or continue with usual care, stratified by service type, size and participation in existing quality improvement initiatives. The intervention consists of point-of-care decision support; a risk communication interface; a clinical audit tool to assess performance on CVD-related indicators; a quality improvement component comprising peer-ranked data feedback and support to develop strategies to improve performance. The control arm will continue with usual care without access to these intervention components. Quantitative data will be derived from cross-sectional samples at baseline and end of study via automated data extraction. Detailed process and economic evaluations will also be conducted. Ethics and dissemination: The general practice component of the study is approved by the University of Sydney Human Research Ethics Committee (HREC) and the ACCHS component is approved by the Aboriginal Health and Medical Research Council HREC. Formal agreements with each of the participating sites have been signed. In addition to the usual scientific forums, results will be disseminated via newsletters, study websites, face-to-face feedback forums and workshops. Trial registration: The trial is registered with the Australian Clinical Trials Registry ACTRN 12611000478910.