Maternal nutrition during gestation provides the nutrients for fetal growth and development. Herein, we investigated the transcriptomic responses of fetal brain and muscle tissues at day 83 of gestation (the end of the first trimester) in female fetuses from heifers assigned in a 2 × 2 factorial design to one of four treatments. The treatments consisted of the main effects of vitamin and mineral supplementation (VTM vs. NoVTM; 113 g·heifer−1·d−1 of mineral premix) and two maternal body weight gain rates (low [LG; 0.28 kg d−1] vs. moderate [MG; 0.79 kg d−1]). RNA sequencing of 31 fetuses revealed 399 unique differentially expressed genes (DEGs) in the brain and 1,273 unique DEGs in the muscle across the six contrasts (false discovery rate ≤ 0.1). Overall, brain DEGs were enriched in tissue morphogenesis and Wnt/phosphatidylinositol 3-kinase–protein kinase B signaling pathways, including WNT2B, WNT5A, and WNT7B (upregulated in VTM_LG vs. NoVTM_LG). In muscle, maternal gain and VTM supplementation modulated the expression of myogenic and epigenetic regulators, including PAX7, MSTN, FOXO3, and DNA demethylation enzymes TET1, TET2, and TET3, highlighting the potential epigenetic programming. These findings demonstrate that maternal diet during the first trimester of gestation alters fetal brain and muscle molecular profiles through genes involved in nutrient-sensing and epigenetic pathways. Together, these results highlight the potential for targeted maternal vitamin and mineral supplementation during early gestation to modulate brain and muscle development. Further research is needed to determine the long-term effects of supplementation on offspring behavior, growth, and efficiency in beef production systems.