A successful treatment of periodontitis depends largely on the successful elimination of the periodontopathogens during non-surgical and surgical mechanical debridement. In this retrospective study, data collection was conducted from 2017 to 2021. The retrospective study included 128 patients with 128 sites of localized periodontitis with pocket depths > 5 mm. The included data were based on sites that received conventional mechanical debridement followed by different adjunctive approaches. In total, 30 patients did not receive any additional treatment (SRP group), 30 patients received SRP + 980 nm diode laser irradiation only (SRP + laser), 30 patients received SRP + 3% hydrogen peroxide irrigation (SRP + H2O2) only and 30 patients received a combined treatment of 3% hydrogen peroxide and 980 nm diode laser irradiation (SRP + H2O2 + laser). Total bacterial counts (TBC) in the periodontal pocket collected for all participants before treatment, immediately after treatment, 6 weeks after treatment, 12 weeks after treatment and 6 months after treatment were statistically analyzed and compared. When the laser was used, irradiation parameters were 10 μsec/pulse duration, 10 kHz, pick power of 10 W, average power of 1 W, irradiation time of one minute with inward and outward movements, and fiber diameter of 320 μm. The irradiation was repeated 3 times/pocket. When hydrogen peroxide was used, the irrigation was conducted for one minute and repeated 3 times. The maximum reduction in TBC was obtained when SRP was coupled with 3% H2O2 irrigation followed by 980 nm diode laser irradiation. After six months of follow-up, a significant reduction in TBC was obtained for the group of SRP + H2O2 + laser when compared to all the other groups, from 7.27 × 107 before intervention to 3.21 × 107 after six months. All three approaches to SRP showed a significant reduction in TBC immediately after treatment. Values were 3.52 × 107, 4.01 × 106, 9.58 × 106, 1.98 × 106 for SRP alone, SRP + diode, SRP + H2O2 and SRP + H2O2 + diode laser, respectively. At 6 months, we saw no significant difference between SRP + laser and SRP + H2O2 with 4.01 × 107 and 4.32 × 107, respectively. This retrospective study reveals that after SRP, irrigation with 3% hydrogen peroxide and irradiation with a 980 nm diode laser within specific treatment protocol can be used as an additional approach to conventional SRP to increase the disinfection of the periodontal pockets > 5 mm.