Chronic periodontitis (CP) and Diabetes mellitus type 2 (DMII) are chronic diseases usually treated by conventional practices. On the other hand, homeopathy can help to treat many different diseases. The aim of this study was to evaluate the effects of homeopathy (H) as an adjunct for non-surgical periodontal therapy (NSPT) in individuals with DMII and CP. Eighty individuals with CP and DM II, of both sexes and aged between 32 and 70 years, participated in this randomized, double-blind, placebo-controlled study. They were divided into two groups: control group (CG) and the test group (TG), and both groups received the NSPT. TG also received homeopathic therapy, including Berberis, Mercurius solubilis/Belladonna/Hepar sulphur and Pyrogenium, while CG received placebo. Clinical and laboratorial examinations were evaluated at baseline and after 1, 6 and 12 months of treatment. Both groups showed significant improvement throughout the study, for most of the parameters studied, but TG presented significative gain of CAL at 1 and 12 months compared to CG. Mean glucose and glycated hemoglobin significantly decreased in both groups after 6 and 12 months. However, there was a significantly further reduction of these parameters in TG, as compared to CG. In conclusion, homeopathy as supplement of NSPT may further improve health condition, including glycemic control, in DMII patients with CP.