Background <p>This cross-sectional study aimed to evaluate occlusal characteristics and masticatory performance in patients with skeletal Class II and Class III malocclusions. Both digital occlusal analysis and standardized bolus analysis were employed to assess functional outcomes in non-surgically treated, surgically treated, and control patients.</p> Methods <p>A total of 133 orthognathic patients (71 female; median age 29.8 years) and 20 controls (9 female; median age 30.0 years) were included. Skeletal malocclusions were categorized as compensated, decompensated, and a separate surgically treated cohort assessed at 5-year postoperative follow-up. Digital occlusal parameters (total tooth contact (TTC), time of occlusion (TOC), occlusal asymmetry (OAS), anterior and posterior tooth contact (ATC, PTC)) were recorded and masticatory performance was assessed using a standardized two-color bolus analysis.</p> Results <p>Non-surgically treated Class II and Class III patients showed significantly reduced TTC, ATC, PTC, and prolonged TOC as well as lower bolus mixing scores compared with controls (<i>p</i> &lt; 0.05). Surgically treated patients at 5-year follow-up exhibited occlusal parameters and bolus mixing scores comparable to controls, indicating normalization of occlusal parameters and masticatory efficiency.</p> Conclusion <p>Skeletal Class II and Class III malocclusions are associated with impaired occlusal function and reduced masticatory efficiency. Orthognathic therapy effectively restores occlusal parameters as well as functional chewing ability in the long term. Combining digital occlusal analysis with bolus analysis provides a comprehensive and objective evaluation of masticatory rehabilitation in orthognathic patients.</p> Trial registration <p>DRKS00025729</p>