Intrauterine growth restriction (IUGR) is associated with several health problems throughout life. Our program aimed at investigating the mechanisms underlying adipose tissue and skeletal muscle development in IUGR pigs, a species of importance for meat industry worldwide and a broadly used biomedical model for adiposity. Pairs of piglets were chosen within litters to have either a medium or a small weight at different stages of gestation or at birth. Because of the hypothesis of a relationship between high-protein (HP) intake in IUGR children and their later adiposity, a subset of IUGR piglets was fed HP formula during suckling, whereas others received a control formula (AP) that mimicked the sow milk composition. In skeletal muscle, the ratio between adult fast and embryonic myosin heavy-chain isoforms was twofold lower in small fetuses than in their medium littermates at 2 days before birth, denoting a lower muscular maturity in IUGR animals. In subcutaneous fat, IUGR counteracted the normal fall of DLK1/Pref-1 expression during gestation, and blunted the temporal increase in expression levels of many differentiating and lipogenic genes; the differences between weight groups were exacerbated around birth. These differences were not associated with modifications in circulating concentrations of energy-producing metabolites between weight groups. The distribution of HP formula to IUGR piglets resulted in accelerated growth rate and in a temporary reduction in adiposity (until weaning) compared with piglets fed AP formula. This was associated with a decrease in the expression levels of genes related to glucose utilization and lipid anabolism in adipose tissues. In 160-day-old pigs having being fed HP formula, adipocytes were enlarged and their lipogenic rates were reduced. Thus, IUGR affects the temporal development of muscle and adipose tissue. Altogether, dietary strategies at different periods should be further tested to modulate stem cell lineage, tissue development and reinstating optimal growth trajectories.