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This mapping review highlights the need for a new paradigm in the understanding of peri-implantitis pathogenesis. The biofilm-mediated inflammation and bone dysregulation (BIND) hypothesis is proposed, focusing on the relationship between biofilm, inflammation, and bone biology. The close interactions between immune and bone cells are discussed, with multiple stable states likely existing between clinically observable definitions of peri-implant health and peri-implantitis. The framework presented aims to explain the transition from health to disease as a staged and incremental process, where multiple factors contribute to distinct steps towards a tipping point where disease is manifested clinically. These steps might be reached in different ways in different patients and may constitute highly individualised paths. Notably, factors affecting the underlying biology are identified in the pathogenesis of peri-implantitis, highlighting that disruptions to the host–microbe homeostasis at the implant–mucosa interface may not be the sole factor. An improved understanding of disease pathogenesis will allow for intervention on multiple levels and a personalised treatment approach. Further research areas are identified, such as the use of novel biomarkers to detect changes in macrophage polarisation and activation status, and bone turnover.