Background/Objectives: Chlorhexidine (CHX)-based mouthwashes are the most commonly used chemical methods as adjuvants for the treatment of peri-implant diseases, but there is a lack of information on their effect on the peri-implant microbiota. The objective of this study was to evaluate the impact of short-time (15 days) self-administered 0.05% and 0.12% commercial chlorhexidine mouthwashes on the peri-implant pocket microbiota of patients with peri-implantitis.

Methods: In this pilot study, we analyzed the microbial composition of peri-implant lesions in 22 patients before and after a 15-day regimen of thrice-daily use of two commercial chlorhexidine mouthwashes containing 0.05% (n = 11) and 0.12% chlorhexidine (n = 11). Microbial samples were collected using paper points, and the taxonomic composition was determined through sequencing of 16S rRNA gene amplicons using Illumina MiSeq.

Results: Although individual responses to chlorhexidine mouthwash treatment varied significantly, neither concentration produced a statistically significant change in the microbial diversity associated with peri-implantitis, suggesting limited treatment penetration into peri-implant lesions. Similarly, changes in the abundance of specific odontopathogens were not statistically significant.

Conclusions: We found no significant differences in the effect of mouthwashes with different chlorhexidine concentrations on the peri-implant microbiota in short-period applications. Even though more extensive studies are required, the observed patient-dependent outcomes of both chlorhexidine mouthwashes on the peri-implant microbiota and their limited effect in controlling the abundance of oral pathogens indicate that prescription of chlorhexidine mouthwashes for the treatment of peri-implantitis should be carried out with caution. Novel presentations of chlorhexidine with better penetration capacities should be developed, as they could offer enhanced benefits in managing peri-implant diseases.