© 2020, Australasian College of Physical Scientists and Engineers in Medicine. Cone-beam computed tomography (CBCT) is an important imaging modality for image-guided radiotherapy and adaptive radiotherapy. Feldkamp–Davis–Kress (FDK) method is widely adopted in clinical CBCT reconstructions due to its fast and robust application. While iterative algorithms have been shown to outperform FDK techniques in reducing noise and imaging dose, they are unable to correct projection-domain artefacts such as beam hardening and scatter. Empirical correction techniques require a holistic approach as beam hardening and scatter coexist in the measurement data. This multi-part proof of concept study conducted in MATLAB presents a novel approach to artefact reduction for CBCT image reconstruction. Firstly, we decoupled the beam hardening and scatter contributions originating from the imaging object and the bowtie filter. Next, a model was constructed to apply pixel-wise corrections to separately account for artefacts induced by the imaging object and the bowtie filter, in order to produce mono-energetic equivalent and scatter-compensated projections. Finally, the effectiveness of the correction model was tested on an offset phantom scan as well as a clinical brain scan. A conjugate-gradient least-squares algorithm was implemented over five iterations using FDK result as the initial input. Our proposed correction model was shown to effectively reduce cupping and shading artefacts in both phantom and clinical studies. This simple yet effective correction model could be readily implemented by physicists seeking to explore the benefits of iterative reconstruction.