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Abstract Background Chronic inflammation and cumulative oxidative stress have been theorized as two common pathways of the interconnection between periodontitis and diabetes. Improvement in oxidizing status has been demonstrated in periodontal patients with diabetes treated with proper non-surgical periodontal treatment. In addition to periodontal treatment, Gaseous ozone therapy has been reported to possess anti-inflammatory properties and the ability to stimulate the endogenous antioxidant defence mechanism. To date, the antioxidant effect of gaseous ozone, in addition with periodontal treatment in diabetic patients, has been examined in only one study. The aim of this study was to determine the efficacy of gaseous ozone therapy as an alternative approach to supporting non-surgical periodontal therapy (NSPT), aimed at improving antioxidant machinery and interfering with ROS production on plasma levels in diabetic individuals diagnosed with moderate or severe periodontitis. Methods One hundred and eighty patients with periodontitis and type 2 diabetes mellitus were randomly assigned to receive non-surgical periodontal treatment (NSPT) plus gaseous ozone therapy (A) NSPT alone (B). Clinical and periodontal parameters -Bleeding on probing (BOP), Periodontal pocket depth (PPD), and Clinical attachment Level (CAL)- and plasma levels of oxidant-antioxidant (TOS- TAOS) levels, glutathione (GSH), and malondialdehyde (MDA) were recorded at baseline and at 3- (T1) and at 6-months (T2) after treatment. Results Both treatments were efficacious in reducing clinical parameters. However, there were no significant differences regarding oxidative stress parameters in group A compared to group B. Conclusions In the present study, gaseous ozone therapy did not enhance the effect of periodontal treatment in reducing oxidative stress in plasma levels of periodontitis patients with type II diabetes. Trial registration The study was registered with ISRCTN1728169 (23/07/2022).