Periodontitis is a highly prevalent chronic inflammatory disease initiated by dysbiotic biofilms and sustained by an exaggerated host immune response, for which scaling and root planing (SRP) remains the cornerstone of therapy. However, mechanical debridement alone may be insufficient to fully resolve inflammation in complex cases and in susceptible patients. In this context, natural products and host modulatory strategies have emerged as potential adjunctive therapies owing to their antimicrobial, anti-inflammatory, antioxidant, and immunomodulatory properties. This systematic review and meta-analysis aimed to evaluate the effectiveness of natural products used as adjuncts to SRP on periodontal clinical outcomes. Comprehensive electronic searches were conducted in MEDLINE/PubMed, Scopus, Web of Science, Cochrane CENTRAL, Embase, SciELO, and Google Scholar through December 2025, and randomized controlled clinical trials were included. Ninety studies were eligible for qualitative synthesis, and thirty-three were incorporated into the meta-analysis. The interventions encompassed a broad spectrum of plant-derived, host-modulatory and nutraceutical compounds, including curcumin, resveratrol, propolis, Aloe vera, green tea catechins, and omega-3 fatty acids, administered via local, systemic, or rinse-based approaches. Meta-analytic findings demonstrated that adjunctive natural products significantly enhanced probing pocket depth (PPD) reduction and clinical attachment level (CAL) gain compared with SRP alone, with additional improvements in gingival inflammation and bleeding outcomes; however, substantial heterogeneity was observed among studies. Overall, natural products provide measurable adjunctive benefits to SRP in the management of periodontitis, although further well-designed, standardized, and long-term randomized trials are necessary to support their routine clinical implementation.