In the present ex vivo experimental study, none of the tested decontamination methods thoroughly eliminated biofilms formed on rough/machined surface implants intraorally. Gauze soaked in saline and the rotary stainless steel instrument showed better cleansability than the ultrasonic scaler in qualitative and quantitative analyses and may be advantageous for cleansing contaminated implant surfaces. Additionally, except for the Er:YAG laser, each of the tested decontamination methods appeared to be more effective on machined surface implants than rough surface implants in terms of reducing biofilms qualitatively and quantitatively. Research on the optimum combination of different cleansing methods that compensate for each method’s respective downsides is urgently required. Further research is needed to elucidate the most effective method to cleanse contaminated implant surfaces.