Purpose: One of the most frequent complications related to dental implants is peri-implantitis, and the characteristics of implant surfaces are closely related to the progression and resolution of inflammation. Therefore, a technical modality that can effectively detoxify the implant surface without modification to the surface is needed. The purpose of this study was to evaluate the effect of erbium-doped: yttrium, aluminium and garnet (Er:YAG) laser irradiation on the microstructural changes in double acid-etched implant surfaces according to the laser energy and the application duration. Methods: The implant surface was irradiated using an Er:YAG laser with different application energy levels (100 mJ/pulse, 140 mJ/pulse, and 180 mJ/pulse) and time periods (1 minute, 1.5 minutes, and 2 minutes). We then examined the change in surface roughness value and microstructure. Results: In a scanning electron microscopy evaluation, the double acid-etched implant surface was not altered by Er:YAG laser irradiation under the condition of 100 mJ/pulse at 10 Hz for any of the irradiation times. However, we investigated the reduced sharpness of the specific ridge microstructure that resulted under the 140 mJ/pulse and 180 mJ/pulse conditions. The reduction in sharpness became more severe as laser energy and application duration increased. In the roughness measurement, the double acid-etched implants showed a low roughness value on the valley area before the laser irradiation. Under all experimental conditions, Er:YAG laser irradiation led to a minor decrease in surface roughness, which was not statistically significant. Conclusions: The recommended application settings for Er:YAG laser irradiation on double acid-etched implant surface is less than a 100 mJ/pulse at 10 Hz, and for less than two minutes in order to detoxify the implant surface without causing surface modification.