Birthweight (BW) is a widely used indicator of neonatal health, with low birthweight (LBW) being linked to higher risks of morbidity and mortality. Timely and precise prediction of LBW is crucial for ensuring newborn health and well-being. Despite recent machine learning advancements in BW classification based on physiological traits in the mother and ultrasound outcomes, maternal status in essential micronutrients for fetal development is yet to be fully exploited for BW prediction. This study aims to evaluate the impact of maternal nutritional factors, specifically mid-pregnancy plasma concentrations of vitamin B12, folate, and anemia on BW prediction. This study analyzed data from 729 pregnant women in Tarragona, Spain, for early BW prediction and analyzed each factor’s impact and contribution using a partial dependency plot and feature importance. Using a super learner ensemble method with tenfold cross-validation, the model achieved a prediction accuracy of 96.19% and an AUC-ROC of 0.96, outperforming single-model approaches. Vitamin B12 and folate status were identified as significant predictors, underscoring their importance in reducing LBW risk. The findings highlight the critical role of maternal nutritional factors in BW prediction and suggest that monitoring vitamin B12 and folate levels during pregnancy could enhance prenatal care and mitigate neonatal complications associated with LBW.