Bacterial colonisation of exposed implant and abutment surfaces can lead to peri-implantitis, a common cause of oral implant failure. When an abutment becomes exposed in the oral environment the typical recommendation is to debride it, to obtain a smoother surface which might be expected to reduce bacterial colonisation. The aim of this study was to evaluate, in vitro, a conventional polishing protocol (PP1) and a simplified polishing protocol (PP2), suggested to have advantages over PP1. The surface morphology and roughness of titanium abutments were characterised at each stage of polishing, and adhesion of oral bacteria was evaluated, using atomic force microscopy, environmental scanning electron microscopy and optical profilometry. PP1 and PP2 methodologies resulted in indistinguishable surface finishes, with fewer scratches than the unmodified surface, and equal roughness values. PP2 resulted in less disruption and less removal of surface material. Early biofilm formation by Streptococcus mutans was reduced on surfaces polished using PP2, but not PP1. Biofilms of Actinomyces naeslundii were more extensive on polished abutment surfaces. Simplified protocol PP2 may be preferable to conventional protocol PP1, since less material is removed, and there is less chance of rough areas remaining. Polishing, however, does not necessarily reduce oral bacterial colonisation.