Background: Periodontitis and type 2 diabetes mellitus (T2DM) are major health problems, especially in low-income populations with little access to dental care. Low-cost models for treatment of periodontal disease have not been tested in controlled studies in low-income populations. Dental prophylaxis, which includes removal of supragingival calculus and plaque, has been shown to arrest the progression of periodontitis. A controlled clinical trial was conducted to determine the effect of dental prophylaxis on periodontitis in T2DM. Methods: Twenty-six patients with T2DM and chronic periodontitis (CP) and 26 without T2DM with CP were selected. Periodontal probing depth (PD), gingival bleeding on probing (BOP), clinical attachment level (CAL), and surfaces with plaque were recorded at baseline and 3, 6, and 9 months after initial treatment. All the participants received instructions on oral hygiene and one session of dental prophylaxis at baseline and every 3 months. Glycated hemoglobin (HbA1c) levels were measured at baseline and every 3 months in patients with T2DM. Results: A significant improvement of PD, BOP, and sites with plaque was observed 3 months after treatment in patients with T2DM (P = 0.001). In controls, mean PD significantly improved after 6 months compared with baseline (P = 0.001). No significant improvement of CAL occurred in either group. No significant differences in periodontal parameters between the groups were detected, and no participant showed progression of CP during the 9-month study period. Dental prophylaxis did not influence HbA1c levels, and no association among HbA1c concentration, pretreatment metabolic status, and severity of CP was found. Conclusion: Routine prophylaxes every 3 months significantly improve periodontal health and prevent progression of CP in both poorly controlled and well-controlled patients with T2DM.