Akkermansia muciniphilais a mucin-degrading bacterium of the intestinal niche, exerting beneficial effects on the host metabolic profile. Accumulating evidence indicatedAkkermansiaas a promising therapeutic probiotic against metabolic disorders such as obesity, type 2 diabetes and cardiovascular diseases. However, in specific intestinal microenvironments, its excessive enrichment may be not beneficial. Conditions like inflammatory bowel disease (IBD),Salmonella typhimuriuminfection or post-antibiotic reconstitution may not benefit fromAkkermansiasupplementation. Furthermore, usingAkkermansiain patients with endocrine and gynecological disorders—such as polycystic ovary syndrome (PCOS) or endometriosis—that have a higher risk of developing IBD, should be critically evaluated. In addition, a cautionary note comes from the neurological field, as the gut microbiota of patients suffering from Parkinson’s disease or multiple sclerosis exhibits a characteristic signature ofAkkermansia municiphilaabundance. Overall, considering these controversial points, the use ofAkkermansiashould be evaluated on an individual basis, avoiding risking unexpected effects.