The gut microbiota comprises a complex bacterial community that resides in the intestine. Imbalances in the gut microbiota can disrupt immune homeostasis, triggering autoimmune diseases including non-infectious uveitis. Despite recent advances, the underlying mechanisms linking the microbiome and uveitis are not fully understood. This review offers a comprehensive analysis of the literature addressing microbiome’s relationship with ocular inflammation. Additionally, it explores the potential of modulating the gut microbiota as a novel therapeutic target. A literature search of published articles related to the role of ocular microbiome in non-infectious uveitis in PubMed and Scopus databases was conducted. The following keywords were used: microbiome, uveitis, and immune-mediate diseases.