Background: The purpose of this study is to assess clinical and microbiologic effects of the non-surgical treatment of peri-implantitis lesions using either an erbium-doped: yttrium, aluminum, and garnet (Er:YAG) laser or an air-abrasive subgingival polishing method. Methods: In a 6-month clinical trial, 42 patients with peri-implantitis were treated at one time with an Er: YAG laser or an air-abrasive device. Routine clinical methods were used to monitor clinical conditions. Baseline and 6-month intraoral radiographs were assessed with a software program. The checkerboard DNA-DNA hybridization method was used to assess 74 bacterial species from the site with the deepest probing depth (PD) at the implant. Non-parametric tests were applied to microbiology data. Results: PD reductions (mean +/- SD) were 0.9 +/- 0.8 mm and 0.8 +/- 0.5 mm in the laser and air-abrasive groups, respectively (not significant). No baseline differences in bacterial counts between groups were found. In the air-abrasive group, Pseudomonas aeruginosa, Staphylococcus aureus, and Staphylococcus anaerobius were found at lower counts at 1 month after therapy (P<0.001) and with lower counts in the laser group for Fusobacterium nucleatum naviforme (P=0.002), and Fusobacterium nucleatum nucleatum (P=0.002). Both treatments failed to reduce bacterial counts at 6 months. Porphyromonas gingivalis counts were higher in cases with progressive peri-implantitis (P<0.001). Conclusions: At 1 month, P. aeruginosa, S. aureus, and S. anaerobius were reduced in the air-abrasive group, and Fusobacterium spp. were reduced in the laser group. Six-month data demonstrated that both methods failed to reduce bacterial counts. Clinical improvements were limited.