BACKGROUND Peri-implantitis is an inflammatory reaction affecting both hard and soft tissues surrounding dental implants. This pathological condition is caused by a polymicrobial aggressive biofilm that colonizes the implant and abutment surface at the peri-implant crevice level. The present in vitro study evaluated different methods of implant surface decontamination and assessed whether the type of the implant surface influences the results. MATERIAL AND METHODS The study was conducted in an in vitro model of peri-implantitis using 30 implants. The implants were divided into 3 equal groups based on the surface characteristics: machined-surface, sand-blasted and acid-etched, and HA-coated. Implants were coated with E. coli biofilm. After an incubation period, they were decontaminated with 4 different methods: sonic scaler application, sonic scaler application with the chemical agent Perisolv® combination, Er: YAG laser treatment, and PDT therapy with methylene blue as a photosensitizer. RESULTS The highest level of decontamination was achieved for machined-surface implants and for the combined chemical-mechanical and Er: YAG laser treatment. CONCLUSIONS The results of our study suggest that the method of implant decontamination should be customized to the type of implant surface.