Aims: First, the study first assessed the impact of maternal exposure to drought in utero on newborn size. Second, the study assessed the effect of prenatal supplementation in offsetting the negative intergenerational effects of maternal exposure to drought in utero on newborn size. Methods: The present study took advantage of a natural experiment from three droughts (1981/82, 1987/88, and 1992/93) of varying severity in rural Malawi to derive maternal exposure to drought in utero based on maternal date of birth. Other data for outcomes and control variables were sourced from the iLiNS-DYAD-M randomized clinical trial. Results: Among infants of mothers exposed to drought in the first trimester, non-significant effects on infant length-for-age Z score (LAZ) were observed for prenatal supplementation with small-quantity, lipid-based nutrient supplements (SQ-LNS) on infant LAZ compared to the iron-folic acid (IFA), controlling for the study covariates. However, prenatal supplementation with multiple micronutrients (MMN) compared to IFA produced significant effects on infant LAZ [-0.853 SD, 95% CI (-1.446: -0.259)]. Conclusions: These findings suggest that prenatal supplementation with SQ-LNS vs IFA or significantly with MMN vs IFA may sometimes not be beneficial for birth outcomes due to intergenerational external shocks in resource-poor, drought-prone settings.