Currently, there is a high prevalence of depression and anxiety worldwide. Recent research about psychopharmacology based on natural products has revealed promising alternatives in mental disorder’s treatment. Medicinal plants are rich in bioactive compounds with beneficial effects on many diseases, among these, mental illnesses. This manuscript presents current research on the role of the gut microbiota in mental health and the potential of some medicinal plants and herbal medicines to modulate this system for anxiety and depression management. Several studies have demonstrated a complex cross talk in the gut–brain axis, which occurs through the autonomic nervous system directly with the enteric nervous system via the vagus nerve, or even through the hypothalamic–pituitary–adrenal axis. Recently, it has been discovered that natural products and their bioactive compounds, especially flavonoids, can alter the composition and diversity of intestinal microbiota, as well as their produced metabolites. Metabolites produced by the microbiota from bioactive substances may be responsible for the anxiolytic and antidepressant effects attributed to their consumption. This interaction between natural products and the gut microbiota is bidirectional. It is necessary for further studies to determine if those compounds themselves exhibit beneficial effects on psychiatric disorders or if these effects are primarily due to the metabolites produced by the gut microbiota fermentation.