This pilot study evaluated the effect of manuka honey as a subgingival adjunct to scaling and root surface debridement in the treatment of periodontitis. This study used a split-mouth design with a 3-month follow-up in seven participants diagnosed with periodontitis Stage III Grade B or C. Root surface debridement was performed on one side of the mouth (control); the other side received debridement plus manuka honey application (test). Clinical parameters were recorded at baseline, 6- and 12-weeks. Gingival crevicular fluid and subgingival plaque were sampled. Microbiological outcomes were analysed using benzoylarginine pnitroanilide assay and polymerase chain reaction assay. Single application of manuka honey to periodontal pockets did not result in additional reduction of pocket depth, improvement of attachment levels or changes in p-nitroaniline enzymes when compared with root surface debridement alone. However, test sites exhibited greater reduction in bleeding than control sites, mean differences 1.3 (95%CI 1.2-1.5) and 1.7 (95%CI 1.5-1.9) at 6-weeks and 12-weeks, respectively. The proportion of mutans streptococci decreased at 6-weeks in test sites but increased at 12-weeks in control sites. Adjunctive application of manuka honey to periodontal pockets improved gingival inflammation but did not demonstrate significant clinical benefits compared with root surface debridement alone.