Objective: The aim of this research was to assess how the application of an oral irrigator modifies the subgingival bacterial flora in patients undergoing periodontal maintenance therapy. We used a qualitative microbiological analysis with a phase contrast microscope that can differentiate a non-pathogenic (immobile) bacterial flora from a pathogenic (mobile). Methods: In this study, 60 patients with a diagnosis of moderate periodontitis were enrolled. They were treated with non-surgical laser-assisted causal therapy and after one month a re-evaluation was performed that established the stabilization of the periodontal pathology. They were instructed in the home oral hygiene protocol with sonic toothbrush, interdental brushes and oral irrigator, and were included in the periodontal maintenance therapy program with a phase contrast microscope control every 6 months. At T0 phase contrast–phase microscopic examinations, the existence of non-pathogenic bacterial flora was displayed in all patients. They were then randomly divided into two groups, A and B. After professional oral hygiene treatment, group B suspended the usage of oral irrigator. Patients of group A, after the professional oral hygiene treatment, were motivated to continue their oral hygiene protocol at home. After three months, the patients underwent microscopic analysis of the bacterial plaque. Results: At T1 in Group B, 90% of patients had undergone a pathogenic bacterial flora change. In group A, in which patients kept using the oral irrigator for the three months, 100% of them showed immobile plaque on phase contrast microscopic analysis. Conclusions: This research showed that oral irrigator in the practice of home hygiene protocols plays a role in the long-term maintenance of a non-pathogenic bacterial flora in periodontal patients.