<p>Gut bacteria generate various metabolites that can significantly affect brain function and behavior through the microbiota–gut–brain axis. This article highlights the role of short-chain fatty acids, tryptophan derivatives, bile acids, and neurotransmitter-like metabolites in regulating neuroinflammation, synaptic plasticity, and neuronal signaling. The article also explores the potential mechanistic pathways through which these chemical signals act on the central nervous system, such as vagus nerve signaling, immune modulation, and blood–brain barrier integrity. The emerging studies suggested that the alterations to metabolites are linked to mental health disorders, including depression, anxiety, and autism spectrum disorders, and neurodegenerative diseases such as Alzheimer’s disease and Parkinson’s disease. Although preclinical and clinical studies provide early promise and insight into the relevance of metabolites in the brain, substantial gaps remain concerning the effects induced by metabolites at the mechanistic level, how the effect is dependent on the context, and how it varies between individuals. The article also highlights and focuses on the translational potential of clinical research, targeting the utilization of microbial metabolites for diagnostics and treatments, including methodological limitations on biomarkers, interventional reliability, and personalized interventions. The review illustrates both the potential and the shortcomings of metabolite-centric research in neuropsychiatric and neurological disorders. Future investigations should prioritize integrative approaches that combine metabolomics, neuroimaging, and clinical outcomes to infer causality and clinical relevance. Overall, metabolites derived from gut bacteria represent an attractive but underappreciated territory for advancing precision medicine for mental health and neurology.</p> Graphical abstract <p></p>