Purpose: Decontamination of the rough surfaces of dental implants is a challenge in the treatment of peri-implantitis. An acceptable cleaning technique must be able to debride and detoxify the surface without traumatizing it. This study assessed the possible implant surface alterations following decontamination with laser, photodynamic therapy (PDT), and application of chlorhexidine (CHX). Materials and Methods: Of 16 dental implants with sandblasted, large-grit, acid-etched surfaces, Aggregatibacter actinomycetemcomitans was cultured on the surfaces of 15 implants for 48 hours. These 15 implants were divided into five groups of three and were subjected to erbium-doped yttrium aluminum garnet (Er:YAG) laser irradiation, 630 nm light-emitting diode and toluidine blue O photosensitizer, 810 nm diode laser, and indocyanine green-based photosensitizer, 2% CHX, and control group (no treatment). One implant remained intact. The morphology and element/phase identification of the implants were studied using scanning electron microscopy (SEM) and energy-dispersive x-ray spectroscopy (EDS), respectively. Results: The SEM images and EDS maps revealed that the decontamination methods did not alter the surface quality of the implants. However, in photodynamic therapy, sodium chloride that remained from rinsing liquid can make an adhesive layer on the surface of the treated implants. Conclusion: Er:YAG laser irradiation and PDT did not alter the surfaces of sandblasted, large-grit, acid-etched implants. Keywords: EDS, implant surface, implant surface alteration, laser, SEM, surface roughness