Objectives The objective of this study was to determine the effect of bone morphogenetic protein‐2 (BMP‐2) mixed with either polyethylene glycol hydrogel or synthetic bone substitute (SBS) on new bone formation in peri‐implant dehiscence defects after 16 weeks of healing. Materials and methods A guided bone regeneration procedure was performed in box‐type peri‐implant defects that were surgically prepared in six beagle dogs. The following four experimental groups were used (i) control (no graft), (ii) SBS+hydrogel, (iii) SBS+BMP‐2/hydrogel and (iv) BMP‐2/SBS+hydrogel. Volumetric analysis using micro‐computed tomography and histomorphometric analysis was performed at 16 weeks post‐operatively. Results The amount of new bone and the total augmented volume did not differ significantly between both BMP‐treated groups and the SBS+hydrogel group (p > .05). Likewise, no histometric differences were observed in the values of new bone area and bone‐to‐implant contact ratio among the three augmentation groups (new bone area: 0.06 ± 0.08, 0.19 ± 0.20, 0.48 ± 0.37 and 0.56 ± 0.60 mm2 [mean ± standard deviation] in groups 1–4, respectively; bone‐to‐implant contact: 9.44 ± 11.51%, 19.91 ± 15.19%, 46.31 ± 29.82% and 42.58 ± 26.27% in groups 1–4, respectively). Conclusion The osteogenic efficacy of BMP‐2 on the regeneration of peri‐implant bone defects was not detectable after 16 weeks regardless of the carrier materials.