Background: A new model of complex diabetes care is provided by a multidisciplinary team which incorporates general practitioner (GP) Clinical Fellows supported by an Endocrinologist and diabetes educator within a community-based general practice setting. This study evaluates the health and clinical benefits of the new model of care, assesses the acceptability of the model to patients, GPs and other health professionals, and examines the cost-effectiveness of the model. Methods/Design: The study is an open, non-inferiority randomised controlled trial with data collected at baseline, 6 and 12 months. Participants are identified from new patients on hospital-based diabetes outpatient clinic waiting lists and new GP referrals. Eligible consenting patients are randomised to either a community practice site (intervention) or a hospital site (usual care). In the intervention model, medical care is led by a GP Clinical Fellow in partnership with an Endocrinologist. Quantitative measures include clinical indicators with HbA1c as the primary outcome; patient-reported outcomes include health-related quality of life, mental health and satisfaction with care. Qualitative methods will be used to explore the perspectives and experiences of patients and providers regarding the new model of care. An economic evaluation will also be undertaken. Discussion: This model of care seeks to improve the quality and safety of healthcare at the interface between the hospital and primary care sectors for patients with complex diabetes. The study will provide empirical evidence about the impact of the model of care on health outcomes, patient and clinician satisfaction, as well as any economic impacts.