Periodontitis is a multifactorial disease that is primarily driven by bacterial biofilm and oral dysbiosis. Listerine^® is a widely used essential-oil-based mouthwash that is well established for its safety and anti-plaque efficacy. However, limited evidence exists regarding its impact on oral microbial composition or its potential effects on gut microbiota. This pilot study aimed to investigate changes in subgingival microbiota and periodontal indices after Listerine^® use and to explore modulation of the gut microbiota. Twelve healthy adults were enrolled, and oral plaque and stool samples were collected at baseline and after a 28-day treatment period. Microbial profiling was performed using next-generation sequencing (NGS) to assess shifts in oral and gut microbiota. The α-diversity and β-diversity indices were computed, and differential abundance analyses were conducted to identify taxa modulated by treatment. NGS-based profiling revealed that oral microbial α-diversity and β-diversity remained stable. Several oral taxa were significantly modulated, including reductions in Gemella haemolysans, Streptococcus oralis and Granulicatella sp., along with increases in Actinomyces viscosus. In the gut microbiota, a modest trend toward reduced Shannon and Simpson diversity indices was observed. Taxonomic shifts included enrichment of the Bacteroides, Phocaeicola and Alistipes species, and decreases in Lachnospiraceae, Intestinibacter sp. and Blautia luti. Despite the limited cohort size and short observation period, these findings suggest that essential-oil-based mouthwash use can transiently modulate both oral and intestinal microbial ecosystems.