We assessed the in vitro activity of Manuka honey against biofilm bacteria in combination with antibiotics and visualized the effect of Manuka honey on bacterial biofilms using scanning electron microscopy. The fractional biofilm eradication concentration (∑FBEC ) index for vancomycin plus Manuka honey against S. aureus IDRL-4284 biofilms was 0.34, indicating a synergistic interaction. The ∑FBEC  index for gentamicin plus Manuka honey against P. aeruginosa PAO1 biofilms was 0.78–0.82, indicating an additive interaction. Scanning electron microscopy of S. aureus IDRL-4284 and P. aeruginosa PAO1 biofilms exposed to Manuka honey and artificial honey containing the same sugar composition as Manuka honey showed that the former had more pronounced effects than the latter on both S. aureus and P. aeruginosa biofilms. Visualized effects included distorted cell morphologies for both bacteria and a decrease in P. aeruginosa extracellular matrix. In conclusion, Manuka honey has a synergistic interaction with vancomycin against S. aureus biofilms and an additive interaction with gentamicin against P. aeruginosa biofilms.