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Childhood obesity is an increasingly severe public health problem, with a prospective impact on health. We propose an exposome approach to identifying actionable risk factors for this condition. Our assumption is that relationships between external exposures and outcomes such as rapid growth, overweight or obesity in children can be better understood through a “meet-in-the-middle” model. This is based on a combination of external and internal exposome-based approaches, i.e. the study of multiple exposures (in our case dietary patterns) and molecular pathways (metabolomics and epigenetics). This may strengthen causal reasoning by identifying intermediate markers that are associated with both exposures and outcomes. Our biomarker-based studies in the STOP consortium suggest (in several ways, including mediation analysis) that Branched-Chain Amino Acids (BCAAs) could be mediators of the effect of dietary risk factors on childhood overweight/obesity. This is consistent with intervention and animal studies showing that higher intake of BCAAs has a positive impact on body composition, glycemia and satiety. Concerning food, of particular concern is the trend of increasing intake of ultra-processed food (UPF), including among children. Several mechanisms have been proposed to explain the impact of UPF on obesity and overweight, including nutrient intake (particularly proteins), changes in appetite or the role of additives. Research from the ALSPAC cohort has shown a relationship between UPF intake and trajectories in childhood adiposity, while UPF was related to lower blood levels of BCAAs. We suggest that an exposome-based approach can help strengthening causal reasoning and support policies. Intake of UPF in children should be restricted to prevent obesity.