1) Background: Fetal Growth Restriction (FGR) has been associated with adverse perinatal outcomes and epigenetic modifications that impact gene expression leading to permanent changes of fetal metabolic pathways and thereby influence development of disease in childhood and adult life. Both clinical and experimental studies showed that maternal nutrition during pregnancy is critical since malnutrition adversely affects fetal growth and physiology. In this study, we investigated the result of maternal food restriction on liver protein expression in Wistar male newborn pups. (2) Materials & methods: Pups born to food restricted mothers were subdivided to FGR and non-FGR groups. Livers of control, FGR and non-FGR groups were analyzed using quantitative proteomics. (3) Results: In total 6665 proteins were profiled. Of these, 451 and 751 were differentially expressed in FGR and non-FGR vs. control respectively, whereas 229 were common between the two groups. Bioinformatics analysis of the differentially expressed proteins (DEPs) in FGR vs. control revealed: induction of the super-pathway of cholesterol biosynthesis and inhibition of thyroid hormone metabolism, fatty acid beta oxidation and apelin liver signaling pathway. In the DEPs of non-FGR vs. control groups there was inhibition of thyroid hormone metabolism, fatty acid beta oxidation and apelin liver signaling pathway as well. (4) Conclusion: This study demonstrates the impact of prenatal food restriction on the proteomic liver profile of FGR and non-FGR offspring underlying the importance of both prenatal adversities and birth weight on liver dependent postnatal disease.