ABSTRACT Objective This study evaluated, in three dimensions, the skeletal effects of two minimally invasive bone‐anchored techniques for surgically assisted palatal expansion, with and without pterygomaxillary disjunction (PD) and nasal septum disinsertion (NSD). Materials and Methods Thirty‐nine patients were retrospectively selected from two centres and assigned to groups: G1 (without PD and NSD) and G2 (with PD and NSD). Cone‐beam computed tomography scans were analysed before and after expansion, using landmarks to assess skeletal changes along the transverse ( X ), vertical ( Y ) and anteroposterior ( Z ) planes. Results Both groups achieved significant transverse expansion, with no intergroup difference ( p = 0.062). G1 showed significant anterior transverse asymmetry (1.4 ± 2.9 mm; p = 0.017). G2 exhibited significant inferior displacement (1.5 ± 1.6 mm right, 1.4 ± 1.5 mm left; p = 0.007, p = 0.009) and anterior displacement (0.8 ± 0.8 mm bilaterally; p = 0.005), although intergroup comparisons were not statistically significant ( p = 0.071 and p = 0.075, respectively). Both groups showed downward displacement of the apices and incisal edges of the upper central incisors, along with mild anterior movement of the posterior nasal spine and dental landmarks. Conclusion The two techniques produced similar skeletal effects across all three‐dimensional axes. A slight clockwise rotation of the maxilla was observed, consistent with previous reports on conventional surgically assisted maxillary expansion. Anterior asymmetry was significant in G1 and may warrant further investigation. Although some displacement tendencies were observed, current evidence does not indicate a clear advantage of one technique over the other.