Maternal nutrition can alter the offspring epigenome at birth. We sought to examine epigenome-wide DNA methylation (DNAme) from a subset of Guatemalan mother-infant dyads from the Women First Preconception Maternal Nutrition Trial (WF). Women were randomized to either: Arm 1) women consumed a daily maternal nutrition supplement (MNS) ≥ 3 months prior to conception until delivery; Arm 2) women consumed the same MNS starting at 12 weeks gestation until delivery; or Arm 3) no MNS. Our findings indicate that maternal MNS was robustly associated with infant DNAme at birth. More specifically, preconception MNS resulted in DNAme changes that differed from the other study arms in biologically relevant pathways suggesting timing of maternal nutrition is important for infant health.