Odontogenic sinusitis is a common maxillary sinus disease. It develops due to the violation of the Schneiderian membrane due to pathological, iatrogenic, or traumatic causes from dental and dentoalveolar structures. The aim of this cohort study was to investigate local and systemic factors associated with Schneiderian mucosal thickening (MT) in patients referred for evaluation of apical periodontitis (AP) and examine their relationship with chronic sinonasal symptoms. Cone-beam computed tomography (CBCT) scans of 197 patients referred for evaluation of endodontic diseases were reviewed. Mucosal thickening in relation to the affected tooth was measured in the coronal section in millimeters at the maximum area perpendicular to the bone. Based on this measurement, the sinus floor was categorized for MT as present (>1 mm) or absent (<1 mm). The sociodemographic and clinical characteristics of the study participants were assessed and compared according to the presence or absence of MT. Furthermore, the relationship between odontogenic sinusitis and chronic sinonasal symptoms was assessed using a chronic sinusitis survey. Male patients had a higher MT than female patients. The presence of periapical lesions and inadequate endodontic treatment were significantly associated with MT. The multivariate logistic regression model showed that the presence of AP increased the odds of MT by approximately 2.5 times (p = 0.028), and nasal obstruction was significantly higher in patients diagnosed with mucosal thickness at different times of their follow-up period (p = 0.018). MT was 2.5 times more likely in the presence of apical periodontitis, and nasal obstruction was the most significant factor associated with the presence of MT.