Substantial evidence has linked the oral microbiome to various systemic diseases, but it remains unclear whether periodontal clinical trials have incorporated omics-level or systemic endpoints. We conducted a dual-modality analysis covering January 2016 to January 2026, including 2,031 Web of Science records and 1,199 interventional periodontal trials from ClinicalTrials.gov. Trial endpoints were classified into three hierarchical tiers using a standardized schema: microbiome/omics, systemic biomarkers, and local clinical parameters. The results showed that although annual publication volume on the oral-systemic axis increased approximately 7-fold, 87.2% of trials still used only local clinical endpoints, only 11.5% included systemic biomarkers, and only 1.3% included microbiome/omics endpoints, with no increase over the decade. Thus, despite substantial research growth, the endpoint structure of periodontal trials has remained largely unchanged, revealing a significant translational gap. Future trials should consider incorporating composite microbial endpoints and biobanking.