Aims <p>This study aimed to assess the three-dimensional effects of orthodontic premolar extraction in Class II division 1 malocclusion cases treated with fixed appliances on maxillary bony changes (alveolar bone thickness and height) and maxillary dental changes (root length and tooth volume).</p> Methods <p>This retrospective cohort study was conducted with 50 adult patients (aged 18–35&#xa0;years) who underwent orthodontic treatment with fixed appliances and extraction of four first premolars. Pre and post treatment cone beam computed tomography scans were analyzed to obtain quantitative measurements of alveolar bone height and thickness, as well as root length and tooth volume.</p> Results <p>There were significant post-treatment reductions in alveolar bone height in almost all teeth, as well as the cervical alveolar bone thickness, particularly on the palatal side of the anterior teeth. Root resorption was evident across all teeth, and central incisors showed the most significant reduction in root length. Tooth volume decreased significantly across all dentitions.</p> Conclusions <p>Premolar extraction in orthodontic treatment is associated with significant changes in alveolar bone height, thickness, root resorption, and tooth volume, particularly in the anterior maxillary region.</p>