The microbiota is known to modulate brain activities via the gut–brain axis, although how the microbiota influences social behaviour is poorly understood. Bruckner et al. sought to investigate the link between the microbiota and a region of the zebrafish brain that regulates social behaviour. Crucially, zebrafish are social animals that are transparent during early development, enabling in vivo visualization of neurodevelopment that is not possible in the mammalian prenatal brain. Using zebrafish that were devoid of microbiota for the first week of their development, the authors found that the presence of microbiota early on is essential for later establishment of normal social behaviour. Mechanistically, during this critical developmental period, the microbiota influences the behaviour and gene expression of microglia, the brain’s resident immune cells, which in turn remodel brain circuits that are homologous to ‘social neurons’ in other vertebrate models. These findings highlight potential therapeutic targets for interventions in neurodevelopmental disorders affecting social behaviour, such as autism spectrum disorder and schizophrenia.