This study evaluated the use of bioactive glass, PerioGlas, after retrograde filling with Super EBA cement in the treatment of periapical bone destruction. Healing outcomes were followed up after endodontic surgery in 186 teeth. Outcomes were divided into two groups according to follow-up time: short- and long-term. The EBA group (n = 110) underwent endodontic surgery and retrograde filling with EBA cement. In the EBA + PerioGlas group (n = 76), PerioGlas was embedded in the bone cavity after retrograde filling. The success rate in the EBA + PerioGlas group was 72% compared with 56% in the Super EBA group at the short-term follow-up and 74% and 84%, respectively, at the long-term follow-up. Healing of periapical bone destruction classified as uncertain at the short-term follow-up was considered successful in two out of three cases at the long-term follow-up. This study found that PerioGlas as bone substitute did not significantly improve endodontic healing outcome.