The systematic review and meta-analysis were undertaken to evaluate the effectiveness of antimicrobial photodynamic therapy (aPDT) in the microbiological alteration beneficial to peri-implantitis treatment. This study is registered with PROSPERO, number CRD42017064215. Bibliographic databases including Cochrane Library, Web of Science, Scopus and PubMed were searched from inception to 8 January 2017. The search strategy was assembled from the following MeSH Terms: "Photochemotherapy," "Dental Implants" and "Peri-Implantitis." Unspecific free-text words and related terms were also included. The Cochrane Collaboration's tool was used to evaluate the risk of bias of included studies. The random-effect model was chosen, and heterogeneity was evaluated using the I test. Three studies met the inclusion criteria. Meta-analysis demonstrated an association between aPDT and reduction in viable bacteria counts for: Aggregatibacter actinomycetemcomitans (OR = 1.31; confidence interval = 1.13, 1.49; P < 0.00001), Porphyromonas gingivalis (OR = 4.08; confidence interval = 3.22, 4.94; P < 0.00001) and Prevotella intermedia (OR = 1.66; confidence interval = 1.06, 2.26; P < 0.00001). A aPDT appears to be effective in bacterial load reduction in peri-implantitis and has a positive potential as an alternative therapy for peri-implantitis.