Background: There is a need for reliable risk assessment tools to better predict peri-implantitis occurrence. This study compared the long-term prognosis value of two models of risk assessment scoring in predicting peri-implantitis. Methods: Seventy-three patients with treated periodontitis representing 232 implants and attending long-term implant maintenance were evaluated. The Periodontal Risk Assessment (PRA) score, which combines only periodontal risk factors/indicators, and the Implant Risk Assessment (IRA) score, which combines both periodontal and implant risk factors/indicators, were calculated during implant maintenance. Peri-implantitis was defined by the presence of probing depth ≥6 mm with bleeding on probing/suppuration and bone level ≥3 mm. Analyses were performed at the patient level. Results: The mean implant follow-up was 6.5 years. Peri-implantitis incidence was 17.8%, and high-risk PRA and IRA percentages were 36.9% and 27.3%, respectively. High-risk PRA and IRA were significantly associated with peri-implantitis incidence, with hazard ratio (HR) = 4.8 and 3.65, respectively. Risk factors/indicators considered separately showed reduced associations with peri-implantitis. Conclusions: The PRA score combining periodontal parameters and IRA score combining both periodontal and implant parameters have comparable value in predicting peri-implantitis. These scores could allow practicians to intercept the risk of peri-implantitis and to manage follow-up modalities in patients with treated periodontitis.