The present study aims to compare the performance of minimally invasive non-surgical and surgical approaches for the therapy of intrabony defects. Twenty-nine patients who presented with intrabony defects were randomly assigned to: 1) a minimally invasive non-surgical technique (MINST) group, or 2) minimally invasive surgical technique (MIST) group. The chair time of each therapeutic procedure was calculated. The probing depth (PD), position of the gingival margin (PGM) and relative clinical attachment level (RCAL) were evaluated at 3 and 6 months after treatments. The patient perception of discomfort/pain experienced during and after therapy and patient satisfaction regarding treatments were also evaluated. Significant PD reductions, RCAL gains, and no changes in the PGM were obtained at 3 and 6 months in MINST and MIST groups (P <0.05). No differences were observed between groups at any time points (P >0.05). Patient-oriented outcomes did not demonstrate differences between therapeutic approaches (P >0.05). Significant higher chair times were required in the MIST group than in the MINST group (P <0.05). Minimally invasive non-surgical and surgical approaches were successfully used for the treatment of intrabony defects and achieved periodontal health in association with negligible morbidity and suitable patient satisfaction. However, non-surgical therapeutic modality presented an advantage in terms of a reduction of treatment chair time.