Implantoplasty can be performed on implants diagnosed with peri-implantitis to facilitate implant decontamination and improve access for oral home care. However, its effect on the mechanical strength of the implant is still uncertain. This study aimed to evaluate the effect of implantoplasty on the fracture resistance of dental implants with various degrees of bone loss, as well as its surface changes. Eighty 4.2 × 13 mm conical connection dental implants were allocated evenly into four groups based on the bone defect morphology: circumferential or semi-circumferential, and 3 or 5 mm vertical height. Half of the implants underwent implantoplasty with tungsten carbide finishing burs. Weight, volume, and surface roughness of the implants were recorded prior to and after instrumentation. All implants were subjected to static loading to failure or fracture and the implant surfaces were then analyzed using optical microscopy. Finite element analysis was carried out to assess the stress pattern on dental implants after implantoplasty. Implantoplasty significantly reduced the fracture resistance of implants with all defect morphologies, aside from those with 3 mm of circumferential bone loss. Implants with 5 mm of peri-implant bone loss also experienced significantly reduced fracture resistance compared to the 3 mm group. Significant decrease in fracture resistance was only observed between the circumferential and semi-circumferential groups with 5 mm of bone loss. Surface roughness was also significantly reduced following implantoplasty. The results from finite element analysis revealed a change in pattern of stress concentration in the implant after implantoplasty. Implantoplasty negatively impacted the fracture resistance of standard diameter dental implants in most scenarios. The increase in exposed implant length resulted in a decrease in fracture resistance. This increase in fracture risk should be considered prior to implantoplasty, especially in implants with more advanced bone loss.