The effect of probiotics in improving or maintaining oral health in orthodontic patients is understudied. The aim of this study is to evaluate the effect of probiotic administration in addition to tooth brushing on clinical gingival inflammation, plaque formation, subgingival microbiota composition, and salivary biomarkers of inflammation in adolescents with fixed orthodontic appliances. The present study is a 6-month, double-blind, two-arm, placebo-controlled, single-center trial, in which 116 adolescent volunteers aged 12–16 years will be recruited from the patients of the orthodontics clinic of the University Hospital of Lille, France. Subjects who meet the eligibility criteria will be allocated to one of the following groups: (i) control: two placebo lozenges per day for 90 days together with regular oral hygiene, (ii) test: two probiotic lozenges per day for 90 days together with regular oral hygiene. Clinical assessment and biological sample collection will be performed at baseline, 3 and 6 months. In addition, compliance outcomes and adverse events will be monitored.