The antimicrobial and anti-biofilm properties of manuka honey (MH) are currently being explored in the treatment of chronic recalcitrant rhinosinusitis. Due to similarities between chronic rhinosinusitis and chronic otitis, manuka honey may find applications in the management of challenging cases of chronic otitis media implicating biofilms. The goal of this study was to investigate the safety of topical application of 4 % MH in the middle ear. Eleven adult female chinchillas had one of their ears randomly assigned to receive transtympanic 4 % MH, while the contralateral ear served as control. Auditory brainstem-evoked response (ABR) was performed before and after MH application. The facial nerve function and vestibular system were assessed clinically. The animals were euthanized one month following the last application, and the cochleae samples were processed for light and scanning electron microscopy. There was no statistically significant differences between ABR thresholds in both control and experimental ears before and after the application of MH. No morphological differences were seen in both groups of cochleae. The outer hair cell counts for both groups were comparable. Our results suggest that 4 % MH appears not toxic to the cells of the cochlea after 4 weeks of application. The long-term effects of prolonged contact on the structure and function of the cochlea however need further investigations.