Purpose: To evaluate the relationship between risk profile assessments of dental implants that have been in function for at least 2 years and peri-implant marginal bone loss during the follow-up period using the Implant Disease Risk Assessment (IDRA) diagram. Materials and Methods: A total of 70 patients, with 170 implants that had been functionally loaded for at least 2 years, had to attend follow-up sessions to be included in the study. Full-mouth plaque index (PI), gingival index (GI), probing depth (PD), bleeding on probing (BoP), and clinical attachment level (CAL) were recorded. Other parameters were also recorded, including peri implant modified plaque index, modified bleeding index, keratinized mucosa width (KMW), and gingival recession (GR). According to the IDRA risk diagram, participants and dental implants were divided into low-, moderate-, and high-risk groups. Marginal bone level (MBL) was measured on periapical radiographs obtained at functional loading (T0) and at the last follow-up session (T1), and mesial and distal marginal bone level changes (ΔMBL) were calculated as T1–T0. Results: A statistically significant correlation was found between the periodontitis history and periodontitis susceptibility regarding IDRA classification at the patient level. Full-mouth GI, PD, and BoP were found to be statistically higher in the high-risk IDRA group. No statistically significant results were found between the mesial and distal ΔMBL of the IDRA risk groups. Conclusions: The IDRA risk level increased especially by periodontitis susceptibility and periodontitis history, but no significant difference was found between risk groups in terms of ΔMBL.