Objective The aim of this study was to evaluate the changes in the nasal mucosa of tracheostomized patients as a result of decreased nasal airflow. Background The effect of tracheostomy on the chest is well established, but the effect on the nasal mucosa and the upper respiratory tract has not been extensively investigated. Patients and methods Thirty-one participants who underwent total laryngectomy or tracheostomy for prolonged intubation were enrolled in the study. Patients were evaluated at 2 and 6 months after tracheostomy endoscopically as regards the color, discharge, crustations, and atrophy of nasal mucosa. The Saccharine test and the methylene blue test were used to assess the mucociliary clearance. Nasal biopsy and histopathological examination with hematoxylin and eosin staining was performed to confirm our findings. Results There was a significant increase in nasal discharge with histopathological increase in mucous-secreting glands by 2 months after tracheostomy and a significant decrease at 6 months postoperatively. The color of the nasal mucosa became more pink 2 months after tracheostomy with no significance, but at 6 months it became more pale with significance. There was a significant improvement in the saccharine times and methylene blue movement toward the nasopharyn × 2 months postoperatively, whereas there was a significant delay in the saccharine times and methylene blue movement at 6 months. On histopathological examination, there was a significant incidence of nasal mucosal atrophy at 6 months. Conclusion There was an increase in the number of mucous glands with their secretion along with an increase in mucociliary clearance of the nose early after tracheostomy or total laryngectomy. However, with time the reverse occurs due to the long-term effect of airflow deprivation on the nasal mucosa with increased incidence of nasal mucosal atrophy as shown by histopathological examination.