The present paper aims to contribute to the methodology of 3D printing in-process colouring and study its implications and impact on the tensile strength and surface quality of the obtained parts. The proposed study was based on a Taguchi L27 DOE plan using standardised EN ISO 527-2 type 1B-shaped specimens, in which four factors on three levels were considered. The obtained results highlight the possibility of using the presented in-process colouring method. Different materials (PLA, PLA+, and PETG) with varying infill densities (15%, 30%, and 50%), colour distribution (33%, 66%, and 99%), and colour pigments (blue, green, and red) were studied and the results highlighted that the most influential parameter on the tensile strength of the parts was infill density, followed by the tested material, colour pigment, and colouring percentage; regarding surface roughness, the most influential parameter was infill density, followed by colouring percentage, colour pigment, and material. Moreover, the values resulting from the Taguchi DOE were compared to uncoloured parts, from which it could be concluded that the colouring of the parts had direct implications (negative for tensile strength and positive for surface roughness).