Cognition is a critical fitness-related trait in vertebrates, yet the variety of mechanisms generating inter- and intra-species variation remains poorly understood. While cognitive differences partially reflect genetic variation, growing evidence implicates the gut microbiome as a modulator of brain function, behaviour, and neural plasticity through conserved gut–brain pathways involving microbial metabolites, neuroactive compounds, and the vagus nerve. Across vertebrates, microbiome composition—shaped by the environment, development, diet, captivity, life history, and seasonality—has been linked to hippocampal function, neurogenesis, neurotransmission, and stress responses, with potential consequences for foraging, cognition, and fitness. We propose that the gut microbiome is not merely a physiological correlate but a dynamic, evolutionarily relevant contributor to cognitive phenotypes on which natural selection can act, offering a framework linking environmental and life-history factors to microbial composition, neurophysiology, cognition, and fitness in wild vertebrates. We also highlight how captivity can alter the microbiome and potentially confound cognitive phenotypes measured in captive animals and emphasise the importance of contributing studies of wild animals in their natural environment to the field. Finally, we outline future directions and what correlational, longitudinal, and field-experimental studies of wild populations can and cannot reveal, and how they can provide a foundation for experimental tests of causality.