Honey is an established traditional medicine with a variety of putative nutritional and health effects, including antibacterial, antioxidant, anti-inflammatory and prebiotic. The aim of the present study was to investigate the safety of consuming manuka honey, UMF® 20+, on healthy individuals by establishing whether UMF® 20+caused an allergic response (as measured by IgE levels), changed major commensal and beneficial microbial groups in the gut and/or affected levels of one of the most common advanced glycation endpoints, Nɛ-(carboxymethyl)-lysine (CML). The study had a randomised, double-blind cross-over design. A total of twenty healthy individuals aged 42–64 years were recruited. We tested two different honeys– a multiflora honey and UMF® 20+, both produced by Comvita New Zealand Ltd (Te Puke, New Zealand). Multiflora honey or UMF® 20+(20 g) was consumed daily for 4 weeks, with a 2-week ‘washout’ period in between. Blood samples were collected every week for each intervention period and used to measure total IgE levels in serum and advanced glycation endproducts – a consequence of methyglyoxal accumulation. Faecal samples were collected at the beginning and end of each 4-week period. DNA was extracted from faecal samples and the levels of a number of microbial groups in the gut, both beneficial and commensal, were analysed. Neither product changed the levels of IgE or CML or altered gut microbial profiles during the trial, confirming that UMF® 20+is safe for healthy individuals to consume. Despite anecdotal evidence suggesting that manuka honey is good for digestive health, we observed no beneficial effects on lower gut bacterial levels with either honey in this healthy population.