We aimed to evaluate the impact of non-surgical periodontal treatment on the salivary expression of leptin, TNF-α, sclerostin, parathyroid hormone, osteoprotegerin, osteopontin, osteocalcin, IL-6, IL-1β and fibroblast growth factor 23 in patients with chronic periodontitis after 1 year of follow-up. Fifteen patients with chronic periodontitis (56.0 ± SD 9.6 years) and 15 subjects with gingivitis (39.7 ± SD 4.4 years) were included in the study. Clinical periodontal parameters, such as probing pocket depth (PPD), clinical attachment level (CAL), % of plaque and bleeding on probing (BOP) were evaluated, and non-stimulated whole saliva was collected from all patients before periodontal treatment and after 1 year of follow-up. A bead-based multiplex assay measured cytokines. In the chronic periodontitis group, periodontal treatment significantly improved clinical parameters and reduced the salivary levels of IL-1β, leptin and TNF-α (p = 0.002, 0.007 and 0.015, respectively). In the gingivitis group, there were also significant improvements in the mean patient %BOP, % Plaque, CAL and PPD. However, there were no significant changes in the cytokine's salivary levels. In conclusion, chronic periodontitis patients showed a significant reduction in the salivary levels of leptin, TNF-α and IL-1β 1 year after periodontal treatment and a significant improvement in their clinical periodontal parameters suggesting that periodontal treatment alone can downregulate important cytokines associated with bone metabolism.