The aims of this study were to identify the microbiological changes in the periodontal pockets following an Er:YAG laser (ERL) irradiation and mechanical debridement to compare the effectiveness of ERL irradiation to mechanical debridement for peri-implantitis treatment through randomized controlled trials. Twenty-three patients with peri-implantitis lesions were treated in either a test group, ERL set at energy level of 100mJ/pulse, frequency of 10Hz, pulse duration was 100µs, and irradiated by three passages, or a control group, with mechanical debridement using an ultrasonic scaler. An examiner measured the following clinical parameters at different stages (a baseline and at 3- and 6-month post-treatment): probing depth (PD), bleeding on probing (BOP), marginal bone loss (MBL), and anaerobic bacteria counts. Linear regression, with generalized estimation equations, was used to compare the clinical parameters and anaerobic bacterial counts at different stages and between groups. The anaerobic bacterial counts significantly decreased within the control group during the follow-ups. At the 6-month follow-up, both groups showed a significant reduction in PD (test group: mean difference of 0.84mm; control group: mean difference of 0.41mm), and the test group showed a significantly higher PD reduction on the buccal site (1.31mm) compared to that of the control group (0.25mm). Both ERL and mechanical debridement treatments led to significant improvements in PD. When mechanical debridement therapy was used, significant anaerobic bacterial count reductions were observed. Future treatment of peri-implantitis should involve a combination of both of these therapies.