The treatment of peri-implantitis implies the decontamination of the surface of the fixture. This study aims to analyze the effect of the erbium-doped yttrium aluminum garnet laser (Er: YAG) on sandblasted and acid-etched (SLA) titanium. 30 titanium SLA disks were divided into three groups. In Group 1, the disks were left intact; on the contrary, both Groups 2 and 3 were irradiated with the Er: YAG laser at different settings, with a pulse duration of 300 μs and a period of 30 s. Group 2 was irradiated at 1 W and 100 mJ/pulse and Group 3 at 4 W and 400 mJ/pulse. The superficial changes at chemical, nano, and microscopical levels were detected through the use of Fourier-transform infrared spectroscopy, atomic force microscopy, and scanning electron microscope. The Kruskal–Wallis test, followed by the Dunn–Bonferroni Post Hoc analysis, detected the presence of statistically significant differences among the groups. The level of significance was p ≤ 0.05. Results showed that Er: YAG irradiation promoted a significant (p < 0.05) increase of oxides and a decrease of microscopical roughness and porosity on SLA disks. However, the protocol tested on group 3 seemed to be too aggressive for the titanium surface, as shown by the presence of micro-cracks and signs of coagulation, melting, and microfractures. In conclusion, Group 2 showed significantly minor surface alterations with respect to Group 3, and the increase of superficial oxide level, the decrease of porosity, and micro-roughness represent a positive alteration that could protect the materials against bacterial adhesion.