Biomechanical cues are instrumental in guiding embryonic development and cell differentiation. Understanding how these physical stimuli translate into transcriptional programs will provide insight into mechanisms underlying mammalian pre implantation development. Here, we explore this type of regulation by exerting microenvironmental control over mouse embryonic stem cells (mESCs). Microfluidic encapsulation of mESCs in agarose microgels stabilized the naïve pluripotency network and specifically induced expression of Plakoglobin (Jup), a vertebrate homologue of β catenin. Overexpression of Plakoglobin was sufficient to fully re establish the naïve pluripotency gene regulatory network under metastable pluripotency conditions, as confirmed by single cell transcriptome profiling. Finally, we found that in the epiblast, Plakoglobin was exclusively expressed at the blastocyst stage in human and mouse embryos – further strengthening the link between Plakoglobin and naïve pluripotency in vivo. Our work reveals Plakoglobin as a mechanosensitive regulator of naïve pluripotency and provides a paradigm to interrogate the effects of volumetric confinement on cell fate transitions.