Background: Hurricane Maria struck Puerto Rico on 20 September 2017 causing catastrophic devastation. Prolonged shortage of food had been a substantial challenge to the residents after Maria. Experiencing food insecurity in utero has been associated with negative health outcomes later in life. We aim to examine whether there is any alteration in the infant gut microbiome that is associated with prenatal food insecurity. Methods: We established a cohort of infants aged 2–6 months who were exposed in utero to Hurricane Maria near San Juan, Puerto Rico and examined the gut microbiota (n = 29) using 16S ribosomal RNA gene sequencing. Results: Among the enrolled infants, 30% of their mothers experienced “post-Maria poor access to food” for at least 1 month during pregnancy. The relative abundance of gut Veillonella spp. is significantly decreased among infants who experienced prenatal food insecurity, compared to those who did not (adjusted p = 0.025). There is no significant difference observed by prenatal food insecurity at the microbial community level in this cohort. Conclusions: Our finding indicated that infants who experienced prenatal food insecurity post hurricane harbor microbial alternations of specific bacterial taxa, which may further influence the microbial maturation and place the individual at a high-risk health trajectory. Impact: We identified that in utero exposure to food insecurity post Hurricane Maria is associated with decreased abundance of Veillonella in the infant gut.Our findings indicated that infants who experienced prenatal food insecurity post hurricane may harbor alterations of specific bacterial taxa in their gut microbiota.This study showed the association between prenatal adverse exposure and alterations of gut microbiome early in life in the context of an extreme event.This study provided insights into the mechanisms underlying prenatal adverse exposure and increased disease risks later in life.Our findings will potentially raise awareness of the negative impact of extreme climate events on the unborn.