For image-guided radiotherapy (IGRT) systems based on cone beam CT (CBCT) integrated into a linear accelerator, the reproducible alignment of imager to x-ray source is critical to the registration of both the x-ray-volumetric image with the megavoltage (MV) beam isocentre and image sharpness. An enhanced method of determining the CBCT to MV isocentre alignment using the QUASAR™ Penta-Guide phantom was developed which improved both precision and accuracy. This was benchmarked against our existing method which used software and a ball-bearing (BB) phantom provided by Elekta. Additionally, a method of measuring an image sharpness metric (MTF₅₀) from the edge response function of a spherical air cavity within the Penta-Guide phantom was developed and its sensitivity was tested by simulating misalignments of the kV imager. Reproducibility testing of the enhanced Penta-Guide method demonstrated a systematic error of <0.2 mm when compared to the BB method with near equivalent random error (s = 0.15 mm). The mean MTF₅₀ for five measurements was 0.278 ± 0.004 lp mm⁻¹ with no applied misalignment. Simulated misalignments exhibited a clear peak in the MTF₅₀ enabling misalignments greater than 0.4 mm to be detected. The Penta-Guide phantom can be used to precisely measure CBCT–MV coincidence and image sharpness on CBCT-IGRT systems.