Objective Nutraceutical agents have been demonstrated as adjuncts for the treatment of several inflammatory diseases. The present study analyzed and compared new nutraceutical agent as an adjunct to Scaling and root planing (SRP) versus SRP alone for the treatment of periodontitis. Materials and methods Sixty-six patients with moderate periodontitis were enrolled. Through a randomized design, the patients were randomly assigned to SRP + nutraceutical agent (test group) or SRP alone (control group). Patients were regularly examined the clinical, inflammatory mediators and visual analogue scale (VAS) changes over a 6-month period. Clinical attachment level (CAL) was the primary outcome variable chosen. Gingival crevicular fluid (GCF) inflammatory mediator change and the impact of treatment on VAS were evaluated through a linear regression model. Results Both treatments demonstrated an improvement in periodontal parameters compared with baseline. After 6 months of treatment, compared with the control group, the test group determined a significant probing depth (PD) ( p  = 0.003) and bleeding on probing (BOP) reduction ( p  < 0.001), while CAL gain was significantly obtained at 30 and 60 days after treatment ( p  < 0.05). In the test group, the level of inflammatory mediators was significantly reduced compared with the control group ( p  < 0.05). The linear regression analysis demonstrated that the nutraceutical agent exerted, in the test group, a significant influence on VAS at 6, 12, 24, and 48 h after treatment ( p  < 0.05). Conclusions Nutraceutical agent resulted in a more significant reduction in clinical, inflammatory mediators and short-term pain compared with SRP alone. Clinical relevance Nutraceutical agent, when combined with SRP, was demonstrated to be effective in reducing periodontal parameters and controlling the levels of inflammatory mediators and pain in patients with periodontitis.