Advancements in the field of implantology have made dental implants a mainstay treatment for both fully and partially edentulous patients. As a result, practitioners need to be able to identify clinical signs of peri-implant disease in its early stages and provide patients with reliable treatment options. The objective of this article is to provide a differential diagnosis of peri-implant lesions, outlining the clinical, radiographic, and histopathologic features of similar benign and malignant conditions. Additionally, two case studies are presented that showcase lesions that mimic peri-implantitis, providing practitioners with practical examples of how to apply the discussed features in a clinical setting. Lesions described in the differential diagnosis include physiologic bone loss, implant fracture, loosened abutments, pyogenic granuloma, peripheral giant cell granuloma, peripheral ossifying fibroma, squamous cell carcinoma, and metastasis extending to the oral cavity.