Periodontitis is an inflammatory condition of the soft and hard tooth-supporting tissues, representing the first cause of tooth loss. In addition to standard mechanical debridement (Scaling and Root Planing, SRP), further approaches have been proposed as adjuncts. The aim of the present randomized clinical trial is to compare the efficacy of ozone or photobiomodulation (PBM) therapy in addition to SRP to treat periodontal disease. According to a split-mouth design, 240 pathological sites, corresponding to 30 periodontal patients, were randomly divided according to the professional oral hygiene protocol performed at baseline (T0) and after 1 (T1), 2 (T2), 3 (T3), 4 (T4), 5 (T5), and 6 (T6) months. A total of 120 sites underwent an ozonized water administration (ozone group), whereas the other 120 sites were treated with photobiomodulation (PBM group), both in addition to SRP. At every timepoint, the following clinical indexes were assessed: Probing Pocket Depth (PPD) (measured on six sites per element), Plaque Index (PI), and Bleeding on Probing (BOP). As regards PPD, significant intergroup differences were noticed from T5, with significantly lower values in the PBM group (p < 0.05), where values further decreased at T6 (p < 0.05). Both PI and BoP generally decreased from baseline to T6 in both groups; a significant difference was found between T0 and T1 among the groups (p < 0.05), with a progressively higher reduction in the PBM group among the time frames of the study, despite intergroup comparisons not being significant (p > 0.05). Both ozone and PBM appear to be effective adjuvant treatments to SRP, obtaining a slightly better outcome for the latter in the long term, with significant differences at T5 and T6 for PPD. However, because of the absence of standardized protocols for PBM considering both therapeutic and research purposes, no definitive conclusions can be reached, and further studies are required.