Scientists are starting to realize that some effects from the animal environment may affect their progeny’s phenotype. These epidemiological evidences of early life programming are very well described in humans and rodents but less documented in bovines, especially in relation to the peri-conceptual period. In fact, as other species the bovine gametes may carry non-genetic information that will impact the survival, the fitness and the phenotype of the embryo-fetus-offspring. Using a peri-pubertal age model we have compared the semen of bulls that we obtained at different ages just after puberty for whole genome DNA methylation, miRNA content and open DNA access regions to identify mechanistic relation to gene expression and DNA methylation in embryos created with the same bulls compared to themselves and mated by IVF to the same heifer several times. A similar experiment was also done with pre-peri and post puber heifers using the same adult bull for repetitive IVF. The overall results indicate that the same pathways are affected in embryos from immature parents. The targeted processes are overwhelmingly associated with cellular metabolism involving mitochondria function and the mTOR pathways amongst others. A very similar conclusion was also observed with embryos obtained from adult mothers under negative energy balance and the resulting calves obtained by surrogate gestations using blood DNA methylation to assess the intergenerational legacy. These results support a metabolic programming across generation associated with an energy deficient status of the parent.