Peri-implant mucositis represents an inflammatory lesion of the mucosa surrounding an endosseous implant, without the loss of the supporting peri-implant bone. Considering its reversible nature, every effort should be made to contrast it, thus avoiding the eventual progression towards peri-implantitis. The aim of the present randomized clinical trial is to evaluate the efficacy of the ozonized water against peri-implant mucositis. A total of 26 patients diagnosed for this latter clinical condition were randomly divided according to the professional oral hygiene protocol performed on the pathological sites at baseline, at T1 (1 month), and T2 (2 months). Group 1 underwent an ozonized water administration (experimental treatment), whereas Group 2 underwent a pure water one (control treatment). Both administrations were performed with the same professional irrigator (Aquolab® professional water jet, Aquolab s.r.l. EB2C S.r.l., Milano, Italy) with no differences in color or taste between the two substances delivered. At each appointment, the following indexes were assessed: the Probing Pocket Depth (PPD), Plaque Index (PI), Bleeding on Probing (BoP), and Bleeding Score (BS). As regards intragroup differences, in Group 1 ozonized water significantly and progressively reduced all the clinical indexes tested, except for PI in the period T1–T2, whereas no significant differences occurred within the control group. Despite this, no significant intergroup differences were generally detected between the two treatments. Accordingly, the role of ozone for the management of peri-implant mucositis deserves to be further investigated.