PurposePresurgical orthopedic plates are widely used for the treatment of cleft lip and palate, which is the most common craniofacial birth defect. For the traditional plate fabrication, an impression is taken under airway-endangering conditions, which recent digital alternatives overcome via intraoral scanners. However, these alternatives demand proficiency in 3D modeling software in addition to the generally required clinical knowledge of plate design.MethodsWe address these limitations with a data-driven and fully automated digital pipeline, endowed with a graphical user interface. The pipeline adopts a deep learning model to landmark raw intraoral scans of arbitrary mesh topology and orientation, which guides the nonrigid surface registration subsequently employed to segment the scans. The plates that are individually fit to these segmented scans are 3D-printable and offer optional customization.ResultsWith the distance to the alveolar ridges closely centered around the targeted 0.1 mm, our pipeline computes tightly fitting plates in less than 3 min. The plates were approved in 12 out of 12 cases by two cleft care professionals in a printed-model-based evaluation. Moreover, since the pipeline was implemented in clinical routine in two hospitals, 19 patients have been undergoing treatment utilizing our automated designs.ConclusionThe results demonstrate that our automated pipeline meets the high precision requirements of the medical setting employed in cleft lip and palate care while substantially reducing the design time and required clinical expertise, which could facilitate access to this presurgical treatment, especially in low-income countries.Supplementary InformationThe online version contains supplementary material available at 10.1007/s11548-023-02858-6.