Insulin-secreting β-cells within the pancreatic islets of Langerhans are lost in patients with type 1 diabetes1. Islets can be generated in vitro by differentiation of human pluripotent stem cells2-5, but understanding of the molecular events governing this process is limited. Here, we use single-cell multiomics to measure chromatin accessibility and transcriptional profiles of 120,064 cells to characterize and delineate maturation of islets from in vitro differentiation. We find distinguishing chromatin accessibility and gene expression signatures as well as dynamic profiles for each major islet cell type produced from in vitro differentiation. Furthermore, based on chromatin accessibility, β, α, and δ cells from in vitro differentiation are more ambiguous in their cellular identity than from isolated primary islets. However, extended time in vitro or with transplantation into mice drives more distinct states of chromatin accessibility for each cell type. Modulation of CTCF expression redirects cell fate from pancreatic islet endocrine to an intestinal enteroendocrine-like cell type. Additionally, knockdown of ARID1B enhances β-cell maturation transcriptionally and by chromatin accessibility. These results provide a comprehensive atlas and insights into cell fate identity and maturation of stem cell-derived islets, which will inform on their utility for therapy and disease modeling6-8.