The interplay between biophysical cues and morphogenesis play a crucial role in embryogenesis, as the mechanical environment and tissue formation are orchestrated flawlessly to support the growth and organization of the developing embryo. Embryonic implantation is a critical process in human development defined by the blastocyst’s adhesion and invasion of the uterus wall. Implantation is a rapid process, in which massive morphological changes occur over the span of a few hours. Thus, it is not surprising that two-third of pregnancies are lost due to implantation failure. Regretfully, immense differences in implantation strategies between mammalian species and ethical boundaries severely limit our ability to study this critical step in human development. In this work we model the critical steps of human embryonic implantation using finite element analysis and produce a micropatterned model of mechano-environment of the process. Within the model embryonic stem cells regained KLF17+/TFCP2L1+ preimplantation markers followed by derivation of GATA6+/SOX17+ primitive endoderm and OCT4+/NANOG+ pluripotent populations. Our work demonstrates that implantation-driven mechanical stress induces partial epithelial to mesenchymal transition (EMT) and expression of N-cadherin in hypoblast cells driving rapid tissue segregation due to differential adhesion. Our work provides a unique set of tools to study early morphogenesis in early human development, and how it can be impacted by genetic, environmental or pharmaceutical cues.