Pluripotent stem cells (PSCs) exhibit extraordinary differentiation potential and are thus highly valuable cellular model systems. However, although different PSC types corresponding to distinct stages of embryogenesis have been in common use, aspects of their cellular architecture and mechanobiology remain insufficiently understood. Here, we investigated how the actin cytoskeleton is regulated in different pluripotency states. We observed a drastic reorganization during the transition from ground-state naïve mouse embryonic stem cells (mESCs) into converted prime epiblast stem cells (EpiSCs). mESCs are characterized by prominent actin-enriched cortical structures that contain cadherin-based cell-cell junctional components, despite not locating at cell-cell junctions. We term these structures 'non-junctional cadherin complexes' (NJCCs) and show that they are under low mechanical tension, depend on the ectodomain but not the cytoplasmic domain of E-cadherin, and exhibit minimal Ca2+ dependence. Active Rac1 was identified as a negative regulator that promotes β-catenin dissociation and NJCC fragmentation. Our data suggests that NJCCs might arise from the cis-association of E-cadherin ectodomain, with potential roles in ground-state pluripotency, and could serve as structural markers to distinguish heterogeneous population of pluripotent stem cells.