: Due to the risk of peri-implantitis, following dental implant placement, this study aimed to evaluate risk indicators associated with marginal bone loss from a retrospective open cohort study of 4,591 dental implants, placed in private practice, with 5- to 10-year follow-up. Furthermore, the prevalence of mucositis and peri-implantitis among the study cohort was evaluated, comparing strict versus relaxed criteria for bleeding on probing. Methods: Periapical radiographs were used to evaluate changes in crestal bone level. Peri-implant soft tissue was evaluated using an ordinal mucosal index in comparison with the conventional binary threshold for bleeding (i.e., present or not). Periodontal probing depth was not evaluated. Linear mixed models were used to evaluate bone level over time, and other risk indicators, at the patient and implant level. Results: Risk indicators found to have a significant impact on bone level included: autoimmune disease, heavy smoking, bisphosphonate therapy, implant location, diameter and design, and the presence of a bone defect at site of implantation. The prevalence of mucositis at the implant level was 38.6% versus 14.2% at 6 to 7 years, when using strict versus relaxed criteria, respectively. The prevalence of peri-implantitis after 6 to 7 years was 4.7% and 3.6% when using strict versus relaxed criteria, respectively. Conclusions: The results of this study identify several risk factors associated with bone loss. Furthermore, the prevalence of mucositis and peri-implantitis was shown to be lower at both the implant and the patient when using strict versus relaxed criteria based on the assessment of oral health surrounding dental implants.