•Maternal inflammatory omega-3 fatty acid markers were associated with child cognition.•Maternal metabolites mediated association between child cognition and risk factors.•Results may inform new targets for intervention to improve child cognition. Poor cognitive outcomes in early childhood predict poor educational outcomes and diminished health over the life course. We sought to investigate (i) whether maternal metabolites predict child cognition, and (ii) if maternal metabolomic profile mediates the relationship between environmental exposures and child cognition. Metabolites were measured using nuclear magnetic resonance-based metabolomics in pregnant women from a population-derived birth cohort. Child cognition was measured at age 2 years. In 662 mother–child pairs, elevated inflammatory markers (β = −2.62; 95% CI −4.10, −1.15; P = 0.0005) and lower omega-3 fatty acid-related metabolites (β = 0.49; 95% CI 0.09, 0.88; P = 0.02) in the mother were associated with lower child cognition and partially mediated the association between lower child cognition and multiple risk factors common to socioeconomic disadvantage. Modifying maternal prenatal metabolic pathways related to inflammation and omega-3 fatty acids may offset the adverse associations between prenatal risk factors related to socioeconomic disadvantage and low child cognition.