This randomized prospective clinical study aims to analyze the differences between the computer-assisted planned implant position and the clinically realized implant position using dynamic navigation. In the randomized prospective clinical study, 30 patients were recruited, of whom 27 could receive an implant (BLT, Straumann Institut AG, Basel, Switzerland) using a dynamic computer-assisted approach. Patients with at least six teeth in their jaws to be implanted were included in the study. Digital planning was performed using cone beam tomography imaging, and the visualization of the actual situation was carried out using an intraoral scan. Two different workflows with differently prepared reference markers were performed with 15 patients per group. The actual clinically achieved implant position was recorded with scan bodies fixed to the implants and an intraoral scan. The deviations between the planned and realized implant positions were recorded using evaluation software. The clinical examinations revealed no significant differences between procedures A and B in the mesiodistal, buccolingual and apicocoronal directions. For the mean angular deviation, group B showed a significantly more accurate value of 2.7° (95% CI 1.6–3.9°) than group A, with a value of 6.3° (95% CI 4.0–8.7°). The mean 3D deviation at the implant shoulder was 2.35 mm for workflow A (95% CI 1.92–2.78 mm) and 1.62 mm for workflow B (95% CI 1.2–2.05 mm). Workflow B also showed significantly higher accuracy in this respect. Similar values were determined at the implant apex. The clinical examination shows that sufficiently accurate implant placement is possible with the dynamic navigation system used here. The use of different workflows sometimes resulted in significantly different accuracy results. The data of the present study are comparable with the published findings of other static and dynamic navigation procedures.