This study investigated the effect of prenatal nutrition on liver metabolome and on body (BW) and liver weight (LW) of Nellore bulls at slaughter. Three treatments were applied in 126 cows during pregnancy: NP—control (mineral supplementation); PP—protein-energy supplementation in the third trimester; and FP—protein-energy supplementation during the entire pregnancy. Offspring BW and LW were evaluated, and a targeted metabolomics analysis was performed on their livers (n = 18, 22.5 ± 1 months of age). Data were submitted to principal component analysis (PCA), analysis of variance (ANOVA), enrichment analysis, and Pearson’s correlation analysis. The phenotypes did not show differences between treatments (p > 0.05). Metabolites PCA showed an overlap of treatment clusters in the analysis. We found significant metabolites in ANOVA (p ≤ 0.05; Glycine, Hydroxytetradecadienylcarnitine, Aminoadipic acid and Carnosine). Enrichment analysis revealed some biological processes (Histidine metabolism, beta-Alanine metabolism, and Lysine degradation). Pearson’s correlation analysis showed 29 significant correlated metabolites with BW and 1 metabolite correlated with LW. In summary, prenatal nutrition did not show effects on the phenotypes evaluated, but affected some metabolites and biological pathways, mainly related to oxidative metabolism. In addition, BW seems to influence the hepatic metabolome more than LW, due to the amount and magnitude of correlations found.