Objective: The primary aim of this current systematic review and meta-analysis was to evaluate the potential microbiological effect of probiotics on the implant microbiota. The secondary aim was to evaluate if probiotics have any effect as an adjunct to non-surgical peri-implant treatment in reducing peri-implant mucositis and peri-implantitis clinical parameters—bleeding on probing, modified Gingival Index, and pocket depth.

Methods: The research focus questions were constructed in accordance with the Participants, Intervention, Comparison, and Outcomes (PICO) criteria, and a PROSPERO protocol was registered. A comprehensive systematic search in MEDLINE via the PubMed, Scopus, and Web of Science Core Collection databases was conducted. Two independent reviewers screened the reports based on the PICO criteria—inclusion and exclusion criteria.

Results: In total, 467 records were identified, and ultimately, 7 papers were included: 3 papers in the qualitative synthesis of microbiological effect and 4 in the meta-analysis synthesis on pocket depth. The data synthesis showed that probiotics had no detectable effect on the implant microflora, and in the following data synthesis, no clinical peri-implantitis variable showed a significantly beneficial effect from probiotics in the test group compared to the control group.

Conclusion: Within the limitations of this review, the oral implant microflora is not affected by probiotics nor do probiotics add any effect to the conventional non-surgical treatment of peri-implant mucositis and peri-implantitis.