We investigated how feed restriction at 50% of maintenance requirements during different stages of gestation affects the transcriptome of newborn goats’ skeletal muscle. Fourteen pregnant dams were randomly assigned into one of the following dietary treatments: animals fed at 50% of maintenance requirement from 8–84 d of gestation and then fed at 100% of maintenance requirement from day 85 of gestation to parturition (RM, n = 6), and animals fed at 100% of maintenance requirement from 8–84 d of gestation and then fed at 50% of maintenance requirement from day 85 of gestation to parturition (MR, n = 8). At birth, samples of offspring's Longissimus muscle were collected for total RNA extraction and sequencing. Our data showed 66 differentially expressed (DE) genes (FDR < 0.05). A total of 6 genes were upregulated and 60 downregulated (FDR < 0.05) in the skeletal muscle of the newborns resulting from treatment RM compared with MR. Our results suggest that the DE genes upregulated in newborn goats’ skeletal muscle from the RM group compared to MR, included genes related to satellite cells, and genes that indicates impaired insulin sensitivity and changes in the composition of intramuscular fat. The DE genes upregulated in newborn goats’ skeletal muscle from the MR group compared to RM, are also related to impaired insulin sensitivity, as well as a predominantly oxidative metabolism and cellular oxidative stress. However, protective mechanisms against insulin sensitivity and oxidative stress may have been augmented in the skeletal muscle of offspring from MR treatment compared to RM, in order to maintain cellular homeostasis.