Objective: To evaluate the effect of routinely used physical decontamination methods on the surface characteristics of zirconia implants and subsequent ability of bacteria to adhere in vitro.Background: Physical decontamination methods commonly used in peri-implantitis therapy and routine implant maintenance can potentially alter zirconia implant surfaces.Methods: Acid-etched zirconia discs were instrumented with titanium curette (TC), plastic curette, air abrasive device, ultrasonic scaler (US) with stainless steel tip. Following instrumentation, surface topography, and surface elemental composition was analyzed using 3D-laser scanning microscopy and energy-dispersive X-ray spectroscopy, respectively. Subsequently, plaque biofilm was cultured on zirconia discs for 48 h and bacterial adhesion assessed using a turbidity test and scanning electron microscopy.Results: A significant difference in surface roughness was observed between the US and control group (p < 0.05). The US and TC caused gray surface discolouration on zirconia discs due to deposition of metallic residue as confirmed by X-ray spectroscopy. No significant difference in bacterial adhesion was noted among all treatment groups (p > 0.05).Conclusion: TC and US with stainless steel tips should be used with caution due to deposition of metallic residue on the surface. Air abrasive devices and plastic curettes caused minimal surface alterations and are, therefore, safer for zirconia implant decontamination.