Peri-implantitis is an inflammatory condition characterized by inflammation in the peri-implant connective tissue and a progressive loss of supporting bone; it is commonly associated with the presence of biofilms on the surface of the implant, which is an important factor in the development and progression of the disease. The objective of this study was to evaluate, using micro-CT, the bone regeneration of surgically created peri-implant defects exposed to a microcosm of peri-implantitis. Twenty-three adult New Zealand white rabbits were included in the study. Bone defects of 7 mm diameter were created in both tibiae, and a cap-shaped titanium device was placed in the center, counter-implanted with a peri-implantitis microcosm. The bone defects received a bone substitute and/or a resorbable synthetic PLGA membrane, according to random distribution. Euthanasia was performed 15 and 30 days postoperatively. Micro-CT was performed on all samples to quantify bone regeneration parameters. Bone regeneration of critical defects occurred in all experimental groups, with a significantly greater increase in cases that received bone graft treatment (p < 0.0001), in all measured parameters, at 15 and 30 days. No significant differences were observed in the different bone neoformation parameters between the groups that did not receive bone grafts (p > 0.05). In this experimental model, the presence of peri-implantitis microcosms was not a determining factor in the bone volume parameter, both in the groups that received regenerative treatment and in those that did not.