The use of a combination of intraoperative cone-beam computed tomography (CBCT) and a navigation system via a spinal software platform for the navigated implantation of oral implants after microsurgical bone transfer is described. Intraoperative data sets were generated using Arcadis Orbic 3D (Siemens, Medical Solutions, Erlangen, Germany) and immediately transferred to the VectorVision(2) navigation system (BrainLAB, Feldkirchen, Germany) via the NaviLink interface. In two patients who underwent microsurgical bone transfer for midfacial reconstruction, implants were placed using intraoperatively acquired CBCT data sets for planning and navigated insertion. In both cases, successful realization of the planned implant sites was achieved by the guidance of the drill, leading to rehabilitation of both patients. CBCT data generated by mobile systems are sufficient for the planning of implant position, and can be used for navigated insertion using tools originally developed for spinal surgery.