Early life is fundamental for brain and microbiota development. Gut microbiota influences brain function. Maternal obesity affects maturation of gut microbiota and is an important predictor of cognitive dysfunction in the offspring. Cognitive decline through life is an increasingly invalidating condition, due to population ageing and the high frequency of predisposing factors (obesity, unhealthy diets). We hypothesize that the negative effects of maternal obesity on cognitive function in the offspring are partly mediated by the microbiota and its metabolites, offering the opportunity for non-invasive risk-screening and -reduction by tailored foods and diets, since earliest life stages. We will use two existing cohorts of children to identify the gut bacteria and metabolites that are related to maternal obesity and offspring’s cognitive development in early, pre-scholar and scholar age. We will use animal models to investigate cause-effect mechanisms, and develop tailored dietary interventions to counteract the effects of maternal obesity on the gut microbiota, improving offspring’s cognition. GUTMOM involves 6 academic centres, a specialised subcontractor and a private industrial collaborator providing project co-funding. The plan includes dissemination and training activities for young scientists. Data management will follow the FAIR principles, and the study will contribute to the future Knowledge Platform on Diet, Intestinal Microbiomics and Health.