Abstract Introduction The complex designs of fixed orthodontic appliances hinder proper access for cleaning, favouring the development of gingival inflammation and white spot lesions around brackets. The aim of this study was to evaluate the effectiveness to avoid these undesirable effects by using two prophylactic methods: Photodynamic Therapy (PDT) and conventional ultrasonic scaler (US), in patients during fixed orthodontic treatment. Materials and methods Twenty patients under orthodontic treatment for at least 15 months were randomly divided into two groups: PDT mediated by methylene blue (MB) and US. Both treatments were applied in repeated doses (four times in intervals of 2 weeks in the beginning of the study (T0), with booster doses at 3, 6 and 9 months, T1, T2 and T3, respectively). Periodontal clinical parameters (full-mouth plaque score (FMPS), full-mouth bleeding score (FMBS) and probing depth (PD)) were recorded as well as the International Caries Detection and Assessment System (ICDAS) index. Samples of subgingival plaque and saliva (for determination of 4 periodontopathogens and mutans streptococci, respectively), were collected at T0 and at the follow-ups of T1, T2 and T3. Results The evolution of FMPS, FMBS, PD, ICDAS scores as well as the counts of periodontopathogens and salivary mutans streptococci was similar after US or PDT implementation. Greatest periodontal scores reduction took place at T1 for FMBS and PD and at T2 for FMPS. Main microbial reduction took place at T1. ICDAS index began to increase from T2. No statistically significant intergroup differences were observed. Conclusions Additional treatment of PDT or US in repeated doses delayed undesired side effects during fixed orthodontic treatment in young patients with low caries risk and signs of gingival inflammation.