The objective of this 9-month clinical study is to assess the impact of one-stage full-mouth disinfection (FMD) on salivary nitrite levels and systemic biomarkers and its correlation with total subgingival bacterial load in obese and non-obese patients with periodontitis. In total, 94 patients (55 obese and 39 non-obese) were initially evaluated, seven were lost during follow-up, resulting in 87 individuals at the end of the study. Outcomes were assessed at baseline, 3, 6, and 9 months post periodontal treatment by FMD. Salivary nitrite levels were determined using Griess reagent. Blood samples were collected to determine C-Reactive Protein (CRP), alkaline phosphatase and fasting blood glucose. Real-time PCR was used to determine the total subgingival bacterial load. FMD protocol resulted in increased salivary nitrite levels at 6- and 9-months post-treatment in the non-obese group (p<0.05). In obese individuals, FMD treatment led to an increase in salivary nitrite levels at 6 months (p<0.05); however, at 9 months, the nitrite levels returned to baseline levels. For both groups, the highest nitrite values were observed at 6 months. In addition, in both groups, FMD was associated with a decrease in biomarkers related to systemic inflammation and cardiovascular diseases, such as CRP (p<0.05) and alkaline phosphatase (p<0.05), and had no impact on the fasting blood glucose. This study demonstrates that obese patients with periodontitis present similar salivary nitrite levels when compared with non-obese individuals. FMD protocol resulted in increases in salivary nitrite levels and was associated with a positive impact on systemic biomarkers, regardless of obesity status.