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Dental implant therapy is a well-accepted treatment modality. Despite good predictability and success in the early stages, the risk of postplacement inflammation in the long-term periods remains an urgent problem. Surgical access and decontamination with chemical and mechanical methods are more effective than antibiotic therapy. The search for the optimal and predictable way for peri-implantitis treatment remains relevant. Here, we evaluated four cleaning methods for their ability to preserve the implant’s surface for adequate mesenchymal stem cell adhesion and differentiation. Implants isolated after peri-implantitis were subjected to cleaning with diamond bur; Ti-Ni alloy brush, air-flow, or Er,Cr:YSGG laser and cocultured with mice MSC for five weeks. Dental bur and titanium brushes destroyed the implants’ surfaces and prevented MSC attachment. Air-flow and laser minimally affected the dental implant surface microroughness, which was initially designed for good cell adhesion and bone remodeling and to provide full microbial decontamination. Anodized with titanium dioxide and sandblasted with aluminum oxide, acid-etched implants appeared to be better for laser treatment. In implants sandblasted with aluminum oxide, an acid-etched surface better preserves its topology when treated with the air-flow. These cleaning methods minimally affect the implant’s surface, so it maintains the capability to absorb osteogenic cells for further division and differentiation.