Background: Mechanical debridement alone may not fully eliminate pathogenic subgingival biofilm, particularly in deep periodontal pockets. Adjunctive therapies are therefore being explored to enhance treatment efficacy. The Perio Protect Method (PPM) employs customized trays to deliver a 1.7% hydrogen peroxide gel, with or without antimicrobials, directly into periodontal pockets, offering localized and sustained antimicrobial action with minimal invasiveness. Objectives: Evaluate the short-term clinical efficacy of PPM as an adjunct to scaling and root planning (SRP) in improving plaque control, gingival health, bleeding on probing (BOP), and probing pocket depth (PPD) in patients with chronic generalized periodontitis. Materials and methods: A prospective interventional study was conducted on 10 systemically healthy patients aged 30–60 years with chronic generalized periodontitis (PPD ≥4 mm in ≥30% of sites). Patients applied a 1.7% hydrogen peroxide gel containing doxycycline (50 mg/mL) in the trays once daily for 15–20 minutes over 3 months. Plaque index (PI), gingival index (GI), BOP, and PPD were recorded at baseline and at 3 months. Data were analyzed using paired t-tests (p < 0.05). Results: PI decreased from 2.7370 ± 0.8277 to 1.2190 ± 0.4015, GI from 2.2620 ± 0.8339 to 0.9710 ± 0.2210, BOP from 2.0400 ± 0.3565 to 0.6970 ± 0.4542, and PPD from 5.6000 ± 0.6992 to 2.6000 ± 0.5164 (all p < 0.001). Conclusion: Adjunctive use of PPM with SRP produced significant short-term reductions in PI, GI, BOP, and PPD, supporting PPM as a beneficial, noninvasive adjunct to conventional periodontal therapy.