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Abstract Background The current study aimed to assess the clinical and radiographic outcomes of the effect of subgingival application of ozonated gel as an adjunct to scaling and root planing (SRP) in diabetic patients with stage III periodontitis. Methods Twenty-four patients with type II diabetes mellitus (DM) were randomized into two groups, with 12 patients in each group. Group I served as the intervention group, receiving both SRP and ozone gel application (SRP + Ozone), while Group II served as the control group, undergoing SRP alone. Clinical attachment level was evaluated as primary outcome, with secondary outcomes including probing pocket depth, full mouth plaque score, full mouth bleeding score, dentinal hypersensitivity, radiographic linear defect depth, radiographic defect angle, and periodontal ligament widening space assessed at 3 and 6 months. Results The results revealed statistically significant intragroup differences between the two groups (p 0.05). The reduction in PD in the SRP + Ozone group at three months was statistically significant (p = 0.04). The SRP + Ozone group showed a significant radiographic improvement compared to the SRP group. The Visual Analogue Scale (VAS) also demonstrated statistically significant differences between the two groups. Glycated hemoglobin (HbA1c) significantly decreased after 6 months, with no significant signifcant differences between groups (p > 0.05). Conclusions Ozone gel is suggested to be a promising potential natural adjunctive therapy for diabetic patients to enhance periodontal health, with no reported adverse effects. Trial registration ID: NCT05538078, Date of Registration: 09/09/2022. ( https://register.clinicaltrials.gov/prs/app/action/DownloadReceipt?uid=U0006D54&ts=3&sid=S000CGX4&cx=g1wreh ).