The purpose of this article was to assess the effectiveness of ozone therapy as an adjunct to mechanical therapy in periodontitis patients. Thirty-two patients diagnosed with generalized periodontitis were selected, with a total of 655 teeth examined. Each patient’s mouth was divided into four quadrants (the split-mouth model) to be randomly treated with four sessions of gaseous ozone or air. The following clinical variables were recorded: the gingival index, the periodontal clinical attachment loss, the Miller’s mobility index and the clinical improvements, as assessed through the visual analog scale (VAS). In addition, the microorganisms were qualitatively compared. After four weeks of treatment, the teeth of the ozone-treated quadrants showed statistically significant reductions in the gingival index and an improvement in the clinical attachment (p < 0.0001). The same treatment also significantly improved mobility by between 70% and 86% compared to the control group (p < 0.0001). Statistically significant differences were also recorded for the VAS (p < 0.0001). In the qualitative study of the subgingival flora, significant differences were observed (p < 0.0001). The overall results of this trial support the view that ozone treatment is effective and well tolerated in cases of generalized chronic periodontitis.