Management of peri-implantitis is becoming an increasing issue for implantologists and periodontists. The need for bone augmentation is more and more frequent, especially in the posterior maxilla requiring sinus augmentation. Peri-implantitis represents a real danger for implants, but to this day, the available literature concerning the impact of this disease on regenerated bone and on maxillary sinus pathology is very limited. This report presents two cases showing bone alterations due to peri-implantitis and its possible impact on maxillary sinus health. In both cases, the causal implant was removed regardless of prior functional endoscopic surgery to restore sinus health, and it was not necessary to implement any reconstruction procedure because bone regeneration occurred naturally. Further research will be necessary to confirm these initial findings.