Background: Peri-implantitis is an infectious disease around dental implants characterized by inflammation of the peri-implant connective tissues and progressive loss of supporting bone, with an estimated prevalence of around 22%. Peri-implantitis microbiota is different from that observed in both periodontitis and healthy implants. Knowledge of this microbiota is crucial for the proper treatment of the disease. Objective: To assess the differences in the oral microbiota in dental implant-bearing patients with and without peri-implantitis. Methods: A search for studies on microbiota and peri-implantitis up to June 2021 was conducted in the following databases: PubMed (MEDLINE, Cochrane Library), Web of Science, Scopus, ProQuest, LILACS, and Google Scholar. For dichotomous outcomes, the effects of the intervention were expressed as odds ratios (OR) using Mantel-Haenszel (MH) method with 95% confidence intervals. Results: Twelve studies with 1324 participants were included in this meta-analysis. Peri-implantitis patients were more likely to be carriers of the following microorganisms: Tannerella forsythia (OR=3. 17, 95% CI: 1. 55 to 6. 51, P<0. 01),Prevotella intermedia (OR=2. 21, 95% CI: 1. 73 to 2. 82, P<0. 001),Treponema denticola (OR=2. 18, 95% CI: 1. 70 to 2. 79, P<0. 001),Porphyromonas gingivalis (OR=2. 04, 95% CI: 1. 16 to 3. 59, P=0. 01),Fusobacterium nucleatum (OR=1. 81, 95% CI: 1. 21 to 2. 72, P<0. 01), and Campylobacter rectus (OR=1. 69, 95% CI: 1. 32 to 2. 17, P<0. 001). In contrast, the bacteria Aggregatibacter actinomycetemcomitans and Streptococcus mitis were more prevalent in peri-implantitis patients but not significantly (P>0. 05). Conclusion: Peri-implantitis modifies the quantitative and qualitative composition of the oral microbiota.