Embryonic neurodevelopment, which occurs in the sterile uterine environment, has recently been shown to be modulated by signals from the maternal gut microbiota. We hypothesised this may occur through microbial signalling to radial glial (RG) cells, which generate cortical neurons, and function as a scaffold along which new-born neurons migrate. Therefore we aimed to study the effect of maternal gut microbiota depletion during pregnancy on RG-led neurodevelopment. Female mice were treated with an antibiotic cocktail prior to and throughout pregnancy to deplete their gut microbiota. Embryonic brains were collected at E15.5 and RG-led neurodevelopmental processes were examined via immunofluorescence. Embryonic CSF and maternal plasma were collected for metabolomic analysis via ultra-performance liquid chromatography-mass spectrometry. Depletion of the gestational maternal microbiota affected embryonic RG-led neurodevelopment, as antibiotic group embryos showed increased numbers of RG progenitor cells in the cortex, and sex-dependant alterations in the density of derived intermediate progenitor cells. Alterations in progenitor cells were associated with changes in the structure of cortical layers. The network of tight junctions expressed in RG apical endfeet at the ventricular interface was also seen to be affected, with no changes in the overall number of RG attachments to the ventricular wall. Finally, maternal antibiotic treatment altered the metabolomic profile of both the maternal plasma and embryonic CSF. In conclusion, we have shown that maternal gut microbiota depletion during pregnancy alters the maternal plasma metabolome and some embryonic CSF metabolites, and leads to alterations in radial glial-led neurodevelopment.