Background: The microbiological status of apparently healed alveolar bone implant sites is unknown. Implant success may be compromised by site-specific persistence of bacterial biofilm co-aggregations contaminating healed alveolar bone. Purpose: The purpose of the present study was to investigate whether extraradicular infection can persist in apparently healed alveolar bone and to develop a surgical debridement strategy that favors implant osseointegration. Materials and Methods: The study was conducted on 32 private practice patients. Seventy-seven microbiological samples were taken from 16 pre-implant extraction sockets, 56 healed post-extraction osteotomies at fixture placement, and five failed fixtures. Two of the healed osteotomy samples were healed retreatment sites. Tissue fluid and bone samples were analyzed by either anaerobic/aerobic culturing or DNA molecular techniques. All patients were treated ad modum Branemark, with a two-stage sterile surgical procedure. A search of the medical and dental literature revealed no evidence-based or best practice recommendations for the use of debridement in implant therapy. Thus, we developed a new technique for the debridement of alveolar bone found to be contaminated by persistent biofilm or planktonic bacteria. Results: The results of the microbiological analysis of 77 bone and effusion samples from 47 implant sites of the 32 patients showed that overall, 32% (n = 25) had bacteria present in the sample. In 16 pre-implant extraction sockets, 69% of samples were positive for the presence of bacteria (n = 11). Of 56 osteotomies with a minimum 3-month healing at fixture placement, 21% revealed a positive culture (n = 12). Two-stage failed fixtures had 100% positive cultures (n = 5) and it was evident from radiographs that all of these failed fixtures had the apical ends close to the former tooth root end. Based on these findings, we have developed a microbiologically based surgical debridement strategy to successfully re-treat early infective failures and to place successful two-stage fixtures. Conclusion: Bacteria can persist as a contaminant in apparently healed alveolar bone following extraction of teeth with apical or radicular pathosis. A new technique for surgical debridement to reduce and limit this bacterial contamination has been described.