Objective.This study aimed to optimise Cone Beam Computed Tomography (CBCT) protocols for head and neck (H&N) radiotherapy treatments using a 3D printed anthropomorphic phantom. It focused on precise patient positioning in conventional treatment and adaptive radiotherapy (ART).Approach.Ten CBCT protocols were evaluated with the 3D-printed H&N anthropomorphic phantom, including one baseline protocol currently used at our centre and nine new protocols. Adjustments were made to milliamperage and exposure time to explore their impact on radiation dose and image quality. Additionally, the effect on image quality of varying the scatter correction parameter for each of the protocols was assessed. Each protocol was compared against a reference CT scan. Usability was assessed by three Clinical Scientists using a Likert scale, and statistical validation was performed on the findings.Main results. The work revealed variability in the effectiveness of protocols. Protocols optimised for lower radiation exposure maintained sufficient image quality for patient setup in a conventional radiotherapy pathway, suggesting the potential for reducing patient radiation dose by over 50% without compromising efficacy. Optimising ART protocols involves balancing accuracy across brain, bone, and soft tissue, as no single protocol or scatter correction parameter achieves optimal results for all simultaneously.Significance.This study underscores the importance of optimising CBCT protocols in H&N radiotherapy. Our findings highlight the potential to maintain the usability of CBCT for bony registration in patient setup while significantly reducing the radiation dose, emphasizing the significance of optimising imaging protocols for the task in hand (registering to soft tissue or bone) and aligning with the as low as reasonably achievable principle. More studies are needed to assess these protocols for ART, including CBCT dose measurements and CT comparisons. Furthermore, the novel 3D printed anthropomorphic phantom demonstrated to be a useful tool when optimising CBCT protocols.