The interest in mental health has increased recently. Anxiety and mood disorders are associated with many disabilities and there is a close relationship between eating disorders and anxiety. Although current medical treatments for anxiety disorders are safer than a few decades ago; the effectiveness in some of them has not improved, they have side effects and can cause addiction. Therefore, the development of new tools to restore mental health without the undesired effects is necessary. Recent studies indicate that patients with generalized anxiety or eating disorders (anorexia nervosa, bulimia nervosa, and binge-eating disorders) show a specific gut microbiota profile, and this imbalance can be partially restored after a single or multi-strain probiotic supplementation. The purpose of this review is to look at the main microbial patterns seen in patients with generalized anxiety and/or eating disorders as well as the importance of probiotics as a preventive or a therapeutic tool in these pathologies. The studies reviewed showed an imbalance of microbial communities in patients with anxiety and with eating disorders. The effect of probiotics in reducing anxiety seems to be more effective the higher the baseline anxiety level of the individual. For eating disorders, the correction of dysbiosis may be associated with the physical and emotional well-being of these subjects. Further study of the intestinal microbiota will enable progress in the study of therapeutic approaches of these areas.