Abstract Aim To assess whether guided bone regeneration (GBR) treatment of peri‐implantitis‐related bony defects could improve healing compared to open flap debridement (OFD) at 36 months. Materials and Methods In a multi‐centre, randomized clinical trial, 32 individuals received OFD (control group [CG]) and 34 GBR treatment (test group [TG]). Radiographic defect fill (RDF), probing pocket depth (PPD), bleeding on probing (BOP) suppuration (SUP), mucosal recession (MREC) and patient‐reported outcomes (PROs) were evaluated at 36 months. Results Fifty individuals attended a supportive peri‐implant therapy program and completed the 36‐month follow‐up. GBR treatment resulted in an RDF of 2.13 ± 1.26 mm compared to 1.64 ± 1.54 mm following OFD ( p = .18). No difference was found in PPD, BOP, SUP, REC or PROs between the groups. Successful treatment (no additional bone loss, PPD ≤ 5 mm, no BOP and no SUP) was achieved in 46.2% in TG and 20% in CG ( p = .053). Treatment results obtained at 12 months were generally maintained up to 36 months. No significant changes were noticed between 12 and 36 months. Conclusions At 36 months, treatment results obtained at 1 year were sustained following both GBR and OFD in patients attending supportive peri‐implant therapy. GBR resulted in more RDF and higher composite treatment success rate than OFD ( ClinicalTrials.gov Identifier [NCT02375750]).