Development of the nervous system is underpinned by changes in gene expression and chromatin configuration during embryogenesis and early postnatal life. To uncover the molecular mechanisms orchestrating cell lineage differentiation and maturation in the enteric nervous system (ENS), we profiled the transcriptome and chromatin accessibility of autonomic neural crest cells (ANCCs) and their progeny in the mouse gut at key developmental stages and adulthood. Integrative analyses defined a differentiation trajectory delineated by ENS progenitors transitioning during development to an enteric glial cell (EGC) state and sequential neurogenic branches driven by shared transcriptional programs. Key loci implicated in neuronal differentiation of early ENS progenitors maintain an open chromatin profile in mature EGCs, enabling these cells to maintain neurogenic potential and return, under appropriate conditions, to developmentally upstream positions of the gliogenic axis. Molecular profiling of lineally marked enteric glial cells (EGCs) in a gut injury model and a novel cell culture system of enteric neurogenesis, demonstrated that neuronal differentiation of mature EGCs is driven by transcriptional programs employed in vivo by early ENS progenitors. Our work advances our understanding of the dynamic regulatory landscape underpinning mammalian ENS development and provides a basis for exploring glial cells as therapeutic agents for the treatment of neural deficits.