Multicolour capability in additive manufacturing could play a key role in certain applications such as surgical training and consumer products. However, the ability to accurately 3D print colours is not well documented and could affect the realism of models produced through these technologies. As a recent system, the Stratasys J750 Digital Anatomy Printer has yet to be analyzed for its colour perception and accuracy, which is quantified through this study. This will allow users of this and similar material jetting systems with an improved understanding of the relationship between digitally applied colours and their result when 3D printed, as well as the influence of certain settings. Thirty-three rectangular prism models with different CMYK and RGB colours, as well as infill materials, were printed on a Stratasys J750 DAP printer. These were scanned on five faces using a Nix Mini 2 handheld colour sensor, documenting readings in CIELAB format. The data were analyzed using the CIEDE2000 colour difference formula, and its recent modifications for 3D printed objects. Results found statistically significant and perceptive differences in colour accuracy among different colours, core materials, and face orientations. It was also observed that the addition of VeroPureWhite as filler material instead of the default SUP706 support improved colour accuracy. The study recommends the following steps to improve colour accuracy: (i) avoid the addition of black (K) manually in CMYK colour space, (ii) use pure white as the base infill material instead of support material, (iii) add a little white (~ 10%–30%) to make samples opaque instead of translucent.