This clinical study aimed to (1) verify the impact of prosthetic abutment height on early peri-implant marginal bone loss (MBL) using peri-apical radiography and (2) analyze the influence of prosthesis design, periodontal status, gender, and prosthesis contour on early peri-implant MBL. Materials and Methods: Patients eligible for this study underwent implant therapies for fixed prosthetic restoration between November 2015 and July 2017 at Kaohsiung Veterans General Hospital. Bone-level implants with platform-switched designs were used. The MBL after implant functional loading for 6-12 months was measured using periapical radiographs. The MBL was affected by the abutment height used as a primary outcome. Other potential covariates-gender, periodontal status, prothesis type, and restoration contour- were controlled. Results: There were 54 patients with 85 implants that included 30 implants with a short prosthetic abutment (< 2 mm, SA) and 55 implants with a long prosthetic abutment (≥ 2 mm, LA). The mean MBL was measured to be 0.38 ± 0.56 mm in the SA group and 0.10 ± 0.15 mm in the LA group. The results showed greater early MBL in the SA group (t = 2.71, p-value = 0.011). Samples in the female group showed a mean MBL of 0.31 ± 0.49 mm (n = 42). More MBL in the female group was noted in our finding (t = 2.94, p-value = 0.005). Conclusion: Within the limitations of the present study, we concluded that prosthetic abutment height < 2 mm would cause more MBL during the first year of functional loading in cement-retained bone-level implants. The female gender could be another risk factor for early MBL, but this requires more investigation. The relationship between prosthetic restoration type, restoration contour, periodontal status, and early peri-implant MBL is not significant.