BACKGROUND: Staged Diabetes Management (SDM) improves glycaemic control and reduces diabetes-related complications in primary care. METHODS: An 18-month randomized controlled cohort study was conducted in two municipalities in the state of Bahia, Brazil, involving 100 patients with Type 2 diabetes in each municipality. In one municipality, healthcare professionals were trained to use SDM customized protocols for clinical decisions and, in the other municipality, no protocols for diabetes care were implemented. We hypothesized that, in the municipality with SDM trained professionals, patients would have better outcomes, including a fall in glycated haemoglobin (HbA(1c)). RESULTS: Improvements in some metabolic parameters were observed in the SDM group, including a 22% decrease in mean random glucose, a significant 15% decrease in mean HbA(1c), a 6% decrease in systolic blood pressure and an 11% decrease in diastolic blood pressure. There were no differences in body mass index and lipid profile. CONCLUSIONS: SDM customized algorithms are effective, practical and easy to use in primary healthcare teams with very limited resources.