KSL-W peptide has demonstrated antibacterial and antifungal activity and inhibitory effects against oral biofilm. This study aimed to check out the effect of chlorhexidine (CLX) or KSL-W peptide-loaded poloxamer 407-based microemulsions for buccal delivery on Fusobacterium nucleatum (F. nucleatum) biofilm. The formulation (F) containing 10% copolymer poloxamer 407 dispersion (1%), 40% oleic acid and 50% PPG-5-CETETH-20 was characterized by polarized light microscopy (PLM), small-angle X-ray scattering (SAXS), rheology, bioadhesive and syringeability; and in the treatment of a biofilm produced by F. nucleatum. The darkfield images obtained by PLM and the SAXS curves with an extended peak indicated that the system was characteristic of microemulsions. In a continuous analysis, microemulsions exhibited Newtonian behavior. In frequency, the oscillatory analysis profile presented predominantly viscous behavior. Bioadhesive force detected in the analysis of F (7.4 ± 1.81 mN˙ s) and syringeability (17.83± 5.97 N · mm) being adequate values for buccal administration. After 4 h, KSL-W-loaded F shown over 20% higher effectiveness than chlorhexidine-loaded microemulsions. In conclusion, the KSL-W-loaded microemulsions showed a considerable reduction in F. nucleatum biofilm formation and presented promising structural properties for buccal drug delivery.