Non-surgical periodontal treatment decreases serum levels of inflammatory cytokines in patients with and without obesity. However, the changes in metabolic parameters in association with these decreases in levels of inflammatory markers by periodontal treatment have not been evaluated in patients with obesity. The aim of this study is to evaluate the short-term changes in systemic inflammatory, lipid, and glucose parameters in the presence of obesity after periodontal treatment. The study included 22 dyslipemic patients with obesity and 24 healthy individuals without obesity with generalized chronic periodontitis. The periodontal parameters, anthropometric measurements, and serum levels of triglyceride, total cholesterol, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, and lipoprotein-a, high-sensitive C-reactive protein, fasting blood glucose, insulin, interleukin-6 (IL-6), tumor necrosis factor-α (TNF-α), and leptin were measured. A homeostasis model assessment of the insulin resistance (HOMA-IR) score was calculated before and 3 months after non-surgical periodontal treatment. Both groups responded well to the periodontal treatment in terms of periodontal parameters. The treatment was also associated with a decrease in serum TNF-α and IL-6 levels and HOMA-IR scores in individuals with obesity and with a decrease in IL-6 levels in patients without obesity. Conversely, there were insignificant decreases in lipid profiles and serum fasting glucose of patients with obesity. The non-surgical periodontal treatment causes a decrease in the levels of some circulating proinflammatory cytokines and may be associated with a decrease in insulin resistance in the obese population.