Manuka honey therapy offers a promising new approach to atrophic rhinitis. An 8-week nasal application significantly improved symptoms, reduced inflammation, and restored healthy nasal tissue. Importantly, honey reshaped the nasal microbiome by enriching beneficial short-chain fatty acid producing bacteria, which correlated with better clinical outcomes. These findings highlight a novel microbiome-driven mechanism and position manuka honey as an effective prebiotic therapy for atrophic rhinitis.