The comprehensive effects of maxillary posterior tooth extraction on the maxillary sinus (MS) morphology remain to be thoroughly elucidated. This retrospective cohort study aimed at evaluating the influence of different extraction indications on the morphological changes in the MS by utilizing cone-beam computed tomography (CBCT). One hundred and seventy-eight of maxillary posterior tooth extractions underwent CBCT scans before and after extraction using 3D Slicer software. Parameters such as maxillary sinus pneumatization (MSP, the primary outcome measure), buccal bone height (BBH), palatal bone height (PBH), mucosal thickness (MT), and other anatomical structures were measured for patients undergoing extraction due to periodontitis, periapical lesions, or tooth fracture. Multiple linear regression analysis was employed to assess the effect of extraction indications on the MS. While the primary outcome, MSP, did not reveal statistically significant differences across various indications for tooth extraction (p > .05), extraction itself resulted in MSP (p < .05). The rate of this pneumatization was influenced by the position of the extraction site (p < .05). Additionally, baseline values of bone height and mucosal thickness showed an inverse correlation with the rate of change in these parameters following tooth extraction (p < .001). Tooth extraction led to increased pneumatization of the maxillary sinus while simultaneously reducing bone height and mucosal thickness. However, these outcomes were not influenced by the reason for tooth extraction.