In this 3-year follow-up study, peri-implant bone loss at bone-level implants was evaluated with two definitive abutment heights: 1 mm and 2.5 mm. Peri-implant bone loss was defined as the distance between the implant shoulder and the first bone-to-implant contact from the time of loading to the 36-month follow-up, estimated using periapical radiographs. The bone loss was increased at the time of follow-up, to 1.30 mm (95% confidence interval [CI]: 0.70-1.89 mm; SD = 1.89) and 0.33 mm (95% CI: 0.11-0.55; SD = 0.59) at 36 months in short and long abutments, respectively. Placement of short abutments induced higher periimplant bone loss at bone-level implants during a peri-implant recall program.