To assess the potential effects of vitamin B₁₂ (B₁₂) and folic acid (FA) supplementation during early stages of pregnancy on the methylome of the offspring from either lactating cows or heifers, 20 Holstein cows, 10 nulliparous (612 ± 46 kg of BW) and 10 multiparous (677 ± 58 kg of BW), once confirmed pregnant (35.7 ± 3.86 d pregnant), were blocked by parity and randomly assigned to either an i.m. weekly injections of a placebo (CTRL) or a solution containing methyl donors (MET). Between pregnancy diagnosis until cows reached 120 d of pregnancy, MET nulliparous cows received 10 mg of B₁₂ and 1,000 mg of FA, whereas MET multiparous cows received 20 mg of B₁₂ and 2,000 mg of FA. After calving, 5 calves randomly selected from each treatment (2 born to primiparous and 3 to multiparous dams) were blood-sampled to isolate peripheral blood mononuclear cells, extract DNA and determine their full methylome. A differentially methylated region (DMR) analysis of CpG islands was performed. Only significant DMR with changes >30% and P < 0.01 were considered. There were more than 2,000 CpG differentially (P < 0.001) methylated between calves born to CTRL and calves born to MET. Within these CpG, 32 and 587 CpG at the promoter and gene regions were hypermethylated, respectively in MET calves. Likewise, 27 and 437 CpG at the promoter and gene regions, respectively, were heavily hypomethylated in MET calves compared with CTRL calves. These changes were more (P < 0.05) marked in calves born to lactating cows than to heifers. Offspring from MET lactating cows had 63 and 464 CpG hypermethylated in the promoter and gene regions, respectively, and 47 and 438 CpG hypomethylated in the promoter and gene regions, respectively. However, supplementing pregnant heifers induced only an hypermethylation of 30 and 161 CpGs in the promoter and gene regions, respectively, and an hypomethylation of 34 and 157 GpG in the promoter and gene regions, respectively. It is concluded that current nutritional recommendations for FA and B₁₂ may be underestimated, and that supplementation of methyl donors early in gestation has important effects on the methylome, especially in lactating dams.