Background and aims <p><i>Clausena excavata</i>Burm. f. (Rutaceae), a tropical plant widely used in traditional medicine, contains bioactive compounds, including essential oils with antibacterial and anti-inflammatory effects. This study explored the development of microemulsions to increase antibacterial activity and reduce the toxicity of <i>C. excavata</i> leaf essential oils.</p> Methods <p><i>C. excavata</i> leaf essential oil was extracted via hydrodistillation, and its chemical composition was analyzed via gas chromatography-mass spectrometry (GC-MS). Microemulsions (F1-F8) were prepared based on pseudoternary phase diagrams. Following thermodynamic stability testing, four formulations (F1-F4) containing Tween^® 80 and ethanol (1:1–4:1) were selected. Among these, F1 and F2 were chosen for optimization into oral spray formulations due to their superior antibacterial activity. Paraben was incorporated as a preservative agent.</p> Results <p>These microemulsions exhibited desirable droplet sizes of 11–13&#xa0;nm, low polydispersity index values, and pH values of 5.8–6.2. The antibacterial activity, evaluated via MIC and MBC assays, revealed that compared with the pure essential oil, microemulsion F1 had significantly lower MIC values 16 and 12 times lower against <i>Streptococcus pyogenes</i> and <i>Klebsiella pneumoniae</i>, respectively (<i>p</i> &lt; 0.05). Moreover, the microemulsion retained anti-inflammatory activity against RAW264.7 cells. Safety assessments via the MTT assay in oral squamous carcinoma cells demonstrated that the microemulsion was less toxic than the pure essential oil.</p> Conclusion <p>These findings suggest that the incorporation of <i>C. excavata</i> leaf essential oil into a microemulsion system enhances its efficacy and safety.</p> Graphical Abstract <p></p>