The purpose of this study was to evaluate skeletal, dentoalveolar and dental changes after Mini-screw Assisted Rapid Palatal Expansion (MARPE) using tooth bone-borne expanders in adolescent patients after analyzing different craniofacial references by Cone Beam Computed Tomography (CBCT) and digital model analysis. This prospective, non-controlled intervention study was conducted on fifteen subjects (mean age 17 ± 4 years) with transversal maxillary deficiency. Pre (T1) and post-expansion (T2) CBCTs and casts were taken to evaluate changes at the premolars and first molar areas. To compare means between two times, paired samples t- or Wilcoxon test were used following criteria. Significant skeletal changes were found after treatment for Buccal Maxillary Width (p < 0.001) in all analyzed teeth with means (SD) of 3.7 (2.0) mm for the first premolar, 4.1 (3.6) mm for the second premolar and 3.7 (2.1) mm for the first molar. Moreover, changes were also found for palatal maxillary width (p < 0.001) with 3.7 (1.8) mm, 3.2 (1.6) mm and 2.2 (2.6), respectively. For dentoalveolar changes, a significant but small buccal bone thickness (BBT) reduction was observed in all teeth with a mean reduction of 0.3 mm for the right and left sides, especially for the distobuccal root of the first molar on the left side (DBBTL1M) [IC95%:(−0.6; −0.2); p = 0.001] with 0.4 (0.4) mm. However, a significant augmentation was observed for the palatal bone thickness (PBT) on the left side. The buccal alveolar crest (BACL) and dental inclination (DI) showed no significant changes after treatment in all the evaluated teeth. MARPE using tooth bone-borne appliances can achieve successful skeletal transverse maxillary expansion in adolescent patients, observing small dentoalveolar changes as buccal bone thickness (BBT) reduction, which was not clinically detectable. Most maxillary expansions derived from skeletal expansion, keeping the alveolar bone almost intact with minor buccal dental tipping.