Objectives The primary aim is to assess differences in accuracy of orthodontic bracket positioning between fully digital indirect bracket bonding (IDB) and conventional direct bracket bonding (DBB). The secondary aims are to assess differences in bracket bonding failures, bracket repositioning need, clinician experience and patient satisfaction. Materials and methods This prospective study was designed as a split-mouth randomized clinical trial. In total, 35 patients were analyzed with a six month follow-up period. Translational and orientational deviations from the planned bracket position were determined. Clinician experience and patient satisfaction were evaluated by means of a survey. Results The difference in translation was 0.34 mm (95% CI: 0.238-0.352, p = 0.017), the difference in orientation was 4.80 & ring; (95% CI: 3.858-5.727, p < 0.001), both in favour of IDB. IDB showed significantly more immediate (IDB: 3.9%, DBB: 0%) and late (IDB: 5.4%, DBB: 2.5%, p = 0.008) bonding failures. Clinicians and patients experienced a shorter clinical chair time with indirect bonding over direct bonding. Conclusions IDB bracket positioning leads to significant smaller translation and orientation deviations from digital IDB planning, than DBB bracket positioning. However, IDB leads to more immediate bonding failures than DBB. The majority of patients preferred IDB over DBB, due to a shorter clinical chair time. Clinical relevance This study adds to the knowledge of IDB in orthodontics and contributes to evidence on this technique. This evidence is applicable in everyday orthodontics, with respect to patient satisfaction and technical limits of IDB.