The burden of diabetes continues to increase in Malaysia, and the public primary health sector has an insufficient number of health care providers well-trained in diabetes care. The Ministry of Health Malaysia collaborated with Steno Diabetes Center to educate primary care doctors and nurses on the fundamentals of clinical diabetes care using a competency-based approach that blends e-learning, classroom-based learning, and clinic-based group work. This programme is called Steno REACH Certificate Course in Clinical Diabetes Care (SRCC). The aim of this study was to assess the effectiveness of the SRCC intervention in improving diabetes-related knowledge, attitudes, skills and clinical practices among non-specialised doctors and general nurses working in public health clinics in Malaysia. This paper presents the study protocol. A quasi-experimental, mixed-methods study based on Solomon’s Four Group Design was applied. Non-specialist doctors and general nurses from ten health clinics were randomly selected to receive the educational intervention. Comparison clinics were purposive selected matching on proxy indicators for quality of diabetes care. The intervention consisted of 50 hours of e-learning, 48 hours of classroom-based learning and approximately 25 hours of work-based learning that covered all main aspects of clinical diabetes care and delivered over a six-month period. Primary outcomes were changes in diabetes-related knowledge, attitudes, skills, and clinical practice. Patients’ perceptions regarding the quality of care provided were classified as a secondary outcome. Other outcome measures included patients' assessment of their chronic disease care and providers' perceptions, attitudes and perceived barriers in care delivery. Results from this study will inform future educational approaches within the Malaysian health system. The study is unique because it evaluated a pertinent public health topic using a very robust methodology.