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Peri-implantitis is an inflammatory lesion leading to bone destruction resulting from bacterial infection and biofilm formation. Treatments of peri-implantitis aim at bacterial controls and decontamination to promote re-osseointegration. The present study aimed to assess the decontamination of biofilm and the osseointegration of titanium discs in a rabbit tibia model. Discs were immersed in culture medium inoculated with Staphylococcus aureus and incubated at 37 °C for 24 h and allocated to different treatments (n = five per group). The decontamination methods were an air-polishing system, 0.12% chlorhexidine rinse, and Er:Yag laser treatments. Each disc from the experimental groups was observed using scanning electron micrography. The rest of the discs were then implanted in four male New Zealand rabbits. Histological and radiographic evaluations were performed. For the quantification of bone density in radiographic data, the fractal dimension (FD) and mean grayscale value (GV) were measured. The Kruskal–Wallis test was used to compare bone density (p < 0.05). Statistically significant differences in FD were observed between the air-polishing treatment with chlorhexidine rinse and the air-polishing treatment with chlorhexidine rinse and Er:Yag laser treatment compared to the contaminated group (p < 0.05). Also, there were statistically significant differences in the results obtained for the group undergoing air-polishing treatment with chlorhexidine rinse and Er:Yag laser treatment compared to the contaminated group (p < 0.05). The decontamination method using air polishing treatment, chlorhexidine rinse, and Er:Yag treatment showed favorable osseointegration with good bone quality. [ABSTRACT FROM AUTHOR]