Imbalances in the gut microbiota occur in various neurological disorders including Alzheimer’s disease (AD), Parkinson’s disease (PD), autism spectrum disorder and depression. Imbalances in key neurotransmitters are associated with the same disorders. This review focuses on the regulatory mechanisms of the intestinal microbiome and its metabolites on cognitive functions and the pathogeneses of these neurodegenerative diseases. The gut microbiota produce neurotransmitters such as glutamate, GABA, serotonin and dopamine or their precursors. These neurotransmitters are not able to cross the blood brain barrier but the precursors are, therefore the gut microbiota is indirectly involved in the regulation of the production of these key neurotransmitters and therefore neuronal activity and cognitive functions of the brain. The findings demonstrate an association between a healthy gut microbiome structure and balanced neurotransmitter levels in the host. Microbial therapy holds huge promise for the treatment of brain disorders. The development of drugs for neurological disorders must also consider effects on the physiology of the gut microbiome.