This study aims to assess the risk of peri-implantitis (PI) onset among different implant systems and evaluate the severity of the disease from a population of patients treated in a university clinic. Furthermore, this study intends to thoroughly examine the surface properties of the implant systems that have been identified and investigated. Data from a total of six hundred and 14 patients were extracted from the Institute of Clinical Dentistry, Dental Faculty, University of Oslo. Subject- and implant-based variables were collected, including the type of implant, date of implant installation, medical records, recall appointments up to 2022, periodontal measurements, information on diabetes, smoking status, sex, and age. The outcome of interest was the diagnosis of PI, defined as the occurrence of bleeding on probing (BoP), peri-implant probing depth (PD) ≥ 5 mm, and bone loss (BL). Data were analyzed using multivariate linear and logistic regression. Scanning electron microscopy, light laser profilometer, and X-ray photoelectron spectroscopy were utilized for surface and chemical analyses. Among the patients evaluated, 6.8% were diagnosed with PI. A comparison was made between two different implant systems: Dentsply Sirona, OsseospeedTM and Straumann SLActive, with mean follow-up times of 3.84 years (SE: 0.15) and 3.34 years (SE: 0.15), respectively. The surfaces have different topographies and surface chemistry. However, no significant association was found between PI and implant surface/system, including no difference in the onset or severity of the disease. Nonetheless, plaque control was associated with an increased risk of developing PI, along with the gender of the patient. Furthermore, patients suffering from PI exhibited increased BL in the anterior region. No differences were observed among the evaluated implant systems, although the surfaces have different topography and chemistry. Factors that affected the risk of developing PI were plaque index and male gender. The severity of BL in patients with PI was more pronounced in the anterior region. Consequently, our findings show that success in implantology is less contingent on selecting implant systems and more on a better understanding of patient-specific risk factors, as well as on implementing biomaterials that can more effectively debride dental implants.