Exact etiology of Atrophic rhinitis (AtR) is yet unknown. Polygenic and polybacterial causes have been implicated in the onset and progression of this disease. AtR doesn’t respond to any particular modality of treatment that targets specific etiology, this describes its multifactorial nature. In this study, we report on a non-randomized control trial on the use of a nasal spray of 10% Manuka honey in patients with AtR attending the out-patient unit of the Department of Otorhinolaryngology and Head Neck Surgery. In this study, we show significant observations: 1. Decreased fetid smell, 2. Thickening of the mucosa, 3. Decreased inflammation with healed mucosal ulcers, 4. Increased concentration of the mucosal glands, 5. Alteration in Nasal microbiome, and 6. Increased expression of SCFA receptors. These changes occurred in response to honey therapy, and are consequent to the resetting of the Nasal microbiome.