This systematic review explores the associations between qualitative/quantitative changes in gut microbiota and psychopathological symptoms or other clinical features in patients with eating disorders (EDs). Secondary outcomes include exploring gut microbiota changes in EDs and potential relationships with psychotropic drug use. A systematic search was conducted across biomedical databases from inception to June 2024 according to PRISMA guidelines. The risk of bias was assessed, and a narrative synthesis was performed due to the heterogeneity of the outcomes. Only findings related to anorexia nervosa (AN) were identified. Ten studies, of which seven were longitudinal, two cross-sectional, and one interventional (N = 350 patients with AN, and 304 HCs), were included. Despite no clear links between diversity metrics and clinical symptoms being observed, specific taxa belonging to phylum Firmicutes, such as Clostridium, Roseburia, Lactobacillus, Faecalibacterium, and Bifidobacterium belonging to Actinobacteriota correlated with ED psychopathology, including anxiety and depressive symptoms. Changes in microbiota were related to anxiety and depressive symptoms, as well as altered eating behaviours by modulating inflammation and insulin pathways through short-chain fatty acids (SCFAs), that also lead to neurotransmitter imbalances. Further studies are required to replicate these finding and to explore whether similar patterns are observed in other EDs.