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Akkermansia muciniphila is considered the “paradigm for next-generation beneficial microorganisms” and has been reported to help alleviat immune-related diseases. Evidence shows that herbal medicine can treat disease by regulating the abundance of A. muciniphila. Recent studies have revealed a link between A. muciniphila and immune-related diseases. Here, we systematically reviewed the association between A. muciniphila, herbal medicine, and immune-related diseases (including inflammatory bowel disease, human immunodeficiency virus, cancer immunotherapy, and immune-related liver injury). We also summarize the potential mechanisms of action of A. muciniphila and offer perspectives for future studies.