OBJECTIVE To evaluate in vitro the changes in implant surface topography and roughness of commercial implants after instrumentation with five decontamination protocols. METHODS Seventy-two titanium implants with a sandblasted and acid-etched (SLA) surface were placed 5 mm supra-crestally. Five groups of twelve implants were instrumented with the following protocols: a metal scaler tip (SCAL), a thermoplastic scaler tip (PEEK), a round titanium brush (RBRU), a tufted brush with titanium bristles (TNBRU), and a glycine-based air-powder abrasive (GLYC). A sixth group with untreated implants was used as control. Scanning electron microscope and confocal laser scanning microscope were utilized to evaluate the changes in the implant surfaces. RESULTS The SCAL caused pronounced macroscopic alterations and damage of the implant surface, the PEEK left remnants of the plastic tip in the implant surface, and both titanium brush groups flattened the thread profile, while minimal alterations were observed in the GLYC. When compared to the control group, the roughness parameters (Sa) in the buccal aspect increased in the thread area of SCAL, and a minor reduction was observed in the PEEK while in the other groups, these values remained unchanged. In the valley areas, however the RBRU, TNBRU, and GLYC experienced a significant reduction (smoothening) indicating different accessibility of the decontamination protocols to the thread and valley. Similarly, the buccal aspects had more pronounced changes than those in the palatal aspect. CONCLUSIONS Within the limitations of this in vitro investigation, the tested protocols induced different macroscopic alterations and surface roughness changes that varied in the thread and valley area.