The purpose of the present study was to evaluate the response to periodontal management in obese individuals with poorly controlled diabetes mellitus (DM) and obese individuals without DM. Changes in clinical and biochemical parameters were also investigated. Seventeen obese patients with poorly controlled DM and 14 obese non-DM patients with generalized chronic periodontitis were enrolled. The anthropometric measurements, periodontal parameters, and serum levels of lipid (triglyceride, high-density lipoprotein cholesterol, total cholesterol, low-density lipoprotein cholesterol) and glucose (fasting plasma glucose IFPGI, insulin, insulin resistance 1111, hemoglobin [Hb]A1c) metabolism, pro-inflammatory mediators (high-sensitivity C-reactive protein, tumor necrosis factor-alpha [TNF-alpha] and Pentraxim-3), and interleukin-6 were measured before and at 3 months, and 6 months after full-mouth scaling and root planing (FM-SRP) together with full mouth disinfection (FMD). A significant reduction in TNF-alpha (P < 0.001) values was observed in both groups following periodontal healing. However, significant changes in FPC (P < 0.05), HbA1C (P < 0.05), and the homeostasis model assessment of IR (HOMA-IR; P < 0.05) were only observed after 3 months in the DM group. Our findings suggest that obesity with or without DM does not seem to be a modifying factor for the clinical outcome of FM-SRP and FMD.