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Summary Human periimplantation development requires the transformation of the naive pluripotent epiblast into a polarized epithelium. Lumenogenesis plays a critical role in this process, as the epiblast undergoes rosette formation and lumen expansion to form the amniotic cavity. Here, we present a high-throughput in vitro model for epiblast morphogenesis. We established a microfluidic workflow to encapsulate human pluripotent stem cells (hPSCs) into monodisperse agarose microgels. Strikingly, hPSCs self-organized into polarized epiblast spheroids that could be maintained in self-renewing and differentiating conditions. Encapsulated primed hPSCs required Rho-associated kinase inhibition, in contrast to naive hPSCs. We applied microgel suspension culture to examine the lumen-forming capacity of hPSCs and reveal an increase in lumenogenesis during the naive-to-primed transition. Finally, we demonstrate the feasibility of co-encapsulating cell types across different lineages and species. Our work provides a foundation for stem cell-based embryo models to interrogate the critical components of human epiblast self-organization and morphogenesis., Graphical abstract, Highlights • High-throughput platform to encapsulate human PSCs in agarose microgels • Human PSCs self-organize into epiblast spheroids and undergo lumen expansion • Lumen expansion increases in primed versus naive human PSCs • Monodisperse co-culture of embryonic and extraembryonic stem cells, In this article, Boroviak and colleagues present a high-throughput platform to encapsulate human PSCs into agarose microgels. Human PSCs undergo lumenogenesis and self-organize into rosette-like structures, similar to the human peri-implantation embryo. Their microgel suspension culture regime provides a foundation for the controlled assembly of stem cell-based embryo models in our own species.