The successful maintenance of crestal bone surrounding dental implants is imperative for long-term implant success. Crestal bone loss is reportedly related to stress. However, early perforation and partial exposure of the implant's covering device are a focus for plaque accumulation, which, if left untreated, may result in inflammation. The objective of this study was to evaluate the crestal bone levels adjacent to submerged and exposed unloaded dental implants during the initial healing phase. In addition, the microbiota around exposed implants were studied. Bilateral implants were placed in the mandible of 10 patients. In one quadrant, the implants were covered by the flap. In the other quadrant, the flap was sutured, leaving the cover screws completely exposed. Standardized periapical radiographs were obtained at implant placement and 4 months later. Radiographs were digitalized, aligned, and analyzed with a computer-assisted method. Cultures were obtained from exposed implant sites. All patients showed more crestal bone loss around exposed dental implants compared to submerged implants. Prevotella sp., Streptococcus beta-hemoliticus, and Fusobacterium sp. were the microorganisms identified in most of the sites. The exposure of the implant covering device created foci for bacterial plaque accumulation, which may have facilitated periimplant crestal bone loss. The initial healing phase follow-up may be critical for implant success.