Background Recommendations for soft tissue management associated with customized bone regeneration should be developed. The aim of this study was to evaluate a new protocol for customized bone augmentation in a digital workflow. Methods The investigators implemented a treatment of three-dimensional bone defects based on a customized titanium mesh (Yxoss CBR (R), ReOSS, Filderstadt, Germany). Patients and augmentation sites were retrospectively analysed focussing on defect regions, demographic factors, healing difficulties and potential risk factors. An exposure rate was investigated concerning surgical splint application, A (R)- PRF and flap design. Results In total, 98 implants could be placed. Yxoss CBR (R) was removed after mean time of 6.53 +/- 2.7 months. Flap design was performed as full flap preparation (27.9%), full flap and periosteal incision (39.7%), periosteal incision (1.5%), poncho/split flap (27.9%) and rotation flap (2.9%). In 25% of the cases, exposures of the meshes were documented. Within this exposure rate, most of them were slight and only punctual (A = 16.2%), like one tooth width (B = 1.5%) and complete (C = 7.4%). A (R)- PRF provided significantly less exposures of the titanium meshes (76.5% no exposure vs. 23.5% yes, p = 0.029). Other parameters like tobacco abuse (p = 0.669), diabetes (p = 0.568) or surgical parameters (mesh size, defect region, flap design) did not influence the exposure rate. Surgical splints were not evaluated to reduce the exposure rate (p = 0.239). Gender (female) was significantly associated with less exposure rate (78,4% female vs. 21.6% male, p = 0.043). Conclusions The results of this study suggest that the new digital protocol including patient-specific titanium meshes, resorbable membranes and bone grafting materials was proven to be a promising technique. To improve soft tissue healing, especially A (R)-PRF should be recommended.