Prenatal origins of heart disease in the adult offspring are established. However, work in species of developmental milestones comparable to humans is lacking, preventing clinical translation. We combine experiments in vivo with those at the isolated organ, cellular, mitochondrial and molecular levels in sheep and chickens, two species with similar cardiovascular developmental milestones to humans. We studied mitochondria-targeted antioxidant intervention with MitoQ against cardiovascular dysfunction programmed by developmental hypoxia, a common complication in human pregnancy. Experiments in sheep determined MitoQ actions on in vivo fetal and adult cardiovascular function through surgical techniques not possible in humans, while those in chicken embryos isolated effects independent of maternal or placental influences. We show that hypoxia generates mitochondria-derived oxidative stress during development of the cardiovascular system, programming endothelial dysfunction and hypertension in the adult offspring. MitoQ treatment during hypoxic development protects against this cardiovascular risk in the adult offspring via enhanced NO signalling pathways, offering plausible intervention.