Emerging evidence suggests that microbial dysbiosis may play a role in pathogenesis of Behçet’s disease (BD). Investigations into the oral microbiota of BD patients have revealed alterations in microbial diversity and abundance compared to healthy controls. Salivary microbiome analyses have shown differences in bacterial composition, with increased abundance of certain taxa which may be related to periodontitis. Similarly, studies on the intestinal microbiota have demonstrated dysbiosis in BD, characterized by reduced diversity of bacteria producing short chain fatty acids, which have key roles in maintenance of the host immune homeostasis, with their systemic and local immunomodulating properties and also epithelial barrier integrity. The potential mechanisms underlying the association between microbial dysbiosis and BD involve bacterial translocation, molecular mimicry, immune dysregulation related to microbial metabolites, and overexpression of toll-like receptors. Clinical studies have explored the modulation of microbiota composition through dietary interventions, showing promising results in reducing disease activity and improving clinical outcomes in BD patients. Although current evidence suggests a possible link between microbial dysbiosis and BD, microbiota composition is inconsistent among studies which also lack uniformity in sampling and sequencing methodologies. Thus, further research is needed to elucidate the role of microbial dysbiosis in BD pathogenesis and its potential as a therapeutic target.