Manufacturing carbon-fibre reinforced polymer (CFRP) composites via different techniques often leads to contrasting surface topographies. Such differences can affect any subsequent surface pre-treatments that are performed and these can ultimately affect joint strength. In the present work, CFRP adherends made using compression moulding or autoclaving were investigated. Pre-treatment techniques of acetone cleaning, plasma treatment, and grit blasting were studied. It was found that the patterned surfaces which had resulted from the vacuum autoclave moulding resulted in improved joint performance when CFRP substrates were bonded together (homogeneous bonding) compared to joints formed with flatter surfaces following compression moulding. However, when CFRP substrates were bonded to flat aluminium alloy substrates (hybrid bonding) the patterned surfaces resulted in inferior joint performance compared to the flatter CFRP substrates. It is proposed that the dissimilarity of surface topographies on the metal and composite substrates negatively influences the strength of the joint.