Dissecting the molecular heterogeneity of the developing human brain is a long-standing ambition of neuroscientists. This has become both a practical and ethically sustainable reality with the advent of cerebral organoids, a 3D in vitro model system of neurogenesis which recapitulates much of the cell type diversity found in the fetal brain. Detailed analysis of cell type-specific biology mandated by the heterogeneity of developing human brain tissue is thus possible without the need of primary samples. Gene regulatory regions, through differential activity, are a key factor for acquisition and maintenance of cell identity and orchestrate intricate developmental processes by directing gene transcription. Here, we describe two experimental methods to isolate distinct cell populations from cortical organoids by means of fluorescence-activated cell sorting, leveraging distinct transcription factor profiles and cell morphological aspects. We assay open chromatin in both live and cross-linked samples using ATAC-seq and validate putative enhancer sequences using luciferase assays. These methods will allow future in-depth epigenomic characterization of human neurogenesis in the context of evolution, health, and disease.