To determine if the treatment of mucositis with mechanical debridement, 0.12% chlorhexidine, and a further application of Lactobacillus reuteri (L. reuteri) will result in an improvement of the clinical and microbiological parameters in comparison to the treatment with mechanical debridement and 0.12% chlorhexidine alone. Fifty dental implants with mucositis in 50 patients were randomly assigned to one of the following groups: mechanical debridement, 0.12% chlorhexidine mouthwash, and the subsequent administration of a probiotic agent (test group) or mechanical debridement and 0.12% chlorhexidine mouthwash (control group). Data were analyzed to determine clinical and microbiological changes during treatment and after a follow-up period of 3months. After the administration of 0.12% chlorhexidine, all clinical parameters improved in the test and the control group, observing a significant decrease in Full Mouth Plaque Index (FMPI), full mouth bleeding on probing (FMBOP), Plaque Index (PI), and bleeding on probing (BOP) at the implant. However, following the administration of probiotics or placebo, the clinical variables, except for probing pocket depth, slightly and progressively increased up to 3months of follow-up, but without reaching baseline levels. From a microbiological point of view, no major alterations of the subgingival microflora were recorded at different time points between groups during the study. Treatment with mechanical debridement, oral hygiene reinforcement, and administration of 0.12% chlorhexidine was effective in reducing mucositis, but it did not always result in complete resolution of inflammation. The administration of probiotics did not seem to provide an additional clinical or microbiological benefit. The use of probiotics does not seem to provide an additional benefit in the treatment of peri-implant mucositis.