Purpose: This study sought to prospectively evaluate changes in marginal bone levels and soft tissue dimensions around platform-switched, Morse taper-connection implants placed with the implant-abutment interface (IAI) at different positions in relation to the alveolar crest. Materials and Methods: Thirty patients in need of single-tooth rehabilitations were randomly assigned to three groups based on the position of the IAI in relation to the alveolar crest at the time of implant placement. Implants in groups 0, 1, and 2 (n = 10 in each group) were placed at the bone level or 1 mm and 2 mm below the buccal aspect of the alveolar crest, respectively. Four months later, the implants were restored with crowns. Clinical parameters were recorded at 4 and 12 months, and marginal bone levels were assessed radiographically at placement, 4 months, and 12 months. Results: Mean marginal bone loss below the implant platform in group 0 implants was 0.18 ± 0.27 mm at 4 months and 0.27 ± 0.45 mm at 12 months. All implants in groups 1 and 2 exhibited no marginal bone loss below the implant platform, since the first bone-to-implant contact was located at or above the implant margin. At 12 months, implants in groups 1 and 2 exhibited greater mean bone loss above the implant platform compared to implants in group 0, but the differences were not statistically significant (group 0, 0.64 ± 0.49 mm; group 1, 0.81 ± 0.31 mm; group 2, 1.20 ± 0.68 mm). Implants in groups 1 and 2 exhibited a statistically significantly higher percentage of implant surfaces with bone on the implant platform compared to group 0 implants (90% versus 35%). Conclusions: In the present study, differences in peri-implant bone responses existed for implants placed with the IAI at different locations in relation to the alveolar crest.