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Fetal neurodevelopment is a critical phase modulated by the maternal microbiome. While certain specific signaling pathways have been identified, the complete signaling network and the spatial and temporal complexity remain largely unknown. Maternal metabolites are essential for fetal growth and certain metabolites are subject to dynamic adaptation during pregnancy. Alteration of maternal microbe richness and diversity, caused by malnutrition, psycho-social distress, and or infection, are cues known to impair fetal neural developmental circuits concomitant with increased risk of cognitive dysfunction later in life. This mini review focuses on the role of maternal microbial metabolites in shaping fetal neurodevelopment.