Purpose: To describe the emerging evidence concerning etiologic factors and pathophysiologic mechanisms involved in peri-implant inflammatory diseases. Materials and Methods: An electronic search for articles published until November 2022 was conducted in MEDLINE by three independent reviewers to identify the manuscripts’ reporting data on etiologic factors and pathophysiologic mechanisms associated with peri-implant diseases. Results: Current evidence suggests that peri-implant mucositis and peri-implantitis are inflammatory conditions linked to a microbial challenge. However, in recent years there has been increasing evidence indicating that certain peri-implant inflammatory conditions may not be primarily related to biofilm-mediated infectious processes but rather to other biologic mechanisms, such as a foreign body response. Conclusions: Current evidence in the dental and medical literature opens new avenues for a more complex interpretation of the etiopathogenetic factors involved in peri-implant diseases. A better understanding of various factors related to the host response, including dysbiosis mechanisms associated with changes in microbiota composition, is necessary for a more precise physiopathologic characterization of these diseases.