Prenatal stress is known to epigenetically program offspring physiology and behaviour, and may become a risk factor for adult complex diseases. To gain insight into the underlying environment-gene interactions, we used proton nuclear magnetic resonance spectroscopy to analyze urinary metabolomes of male and female adolescents who were in utero during the 1998 Quebec Ice Storm. Metabolomic profiles in adolescent groups were found to be significantly different. Higher prenatal stress exposure generated alterations in metabolic pathways involved in energy metabolism and protein biosynthesis, such as branched-chain amino acid synthesis, alanine metabolism, and ketone body metabolism. Dysregulation of energy and protein metabolism suggests an increased risk of metabolic diseases like insulin resistance, diabetes, and obesity. These findings are consistent with prior observations of physiological phenotypes from this cohort. Understanding the impact of natural disasters on health risks will provide new and improved therapeutic strategies to mitigate stress-associated adverse health outcomes. Using metabolomic biomarkers may also assist in the prediction and prevention of these adverse outcomes.