Micronutrients, which are important for brain development, influence fetal brain development, but how prenatal micronutrient deficiency affects early brain development is still not fully understood. The aim of this research is to determine the learnable absence of maternal micronutrient deficiency relations and fetal brain development biomarker(s) at birth, employing an integrated maternal-placental-fetal approach. The study illustrates coordinated changes in the fetal neurodevelopmental signaling deficiency related to the maternal micronutrient deficiency in neurotrophic, growth, and myelination biomarkers in the placental and cord blood of the myelination deficient maternal micronutrient. The multivariate analyses of the fetal biomarker profiles according to maternal micronutrient absence resulted in distinct and clear stratification which was indicative of the developmental lag of certain micronutrients employed the functional modeling of the non-linear relations. Of the fetal neurodevelopmental biomarkers, the absence of maternal micronutrients is indicative of the early structural vulnerabilities of the developing fetus. The research also highlighted the importance of nutritional interventions that are targeted during the prenatal period.