The embryonic body-plan is established during the process of gastrulation, when pluripotent stem cells (ESCs) of the epiblast differentiate into the three embryonic germ lineages in a highly spatio-temporally controlled manner. This spatio-temporal patterning is driven by feedback between various key signalling pathways, initiated by the growth factor BMP4. Despite being a critical stage of development, how cell fate choices are made during gastrulation and how cellular identities are subsequently remodelled at the transcriptomic and epigenetic level is still not well understood. We used 2D and 3D ESC-based models of human gastrulation to perform live cell tracking, quantitative single-cell analysis, and multi-omics studies to determine that the transcription factor GATA3 is rapidly upregulated by the BMP4 signalling pathway to play a crucial role in early gastrulation. We found that GATA3 mediates an early commitment to exit pluripotency through a regulatory feedback network. After this point of commitment, GATA3 acts to remodel the cellular epigenetic landscape by both activating regulatory regions associated with the new identity and silencing regions associated with pluripotency and alternate lineages. Additionally, GATA3 drives patterning of the ESC population through upregulation of growth factor WNT3, forming the mechanistic link between the BMP pathway and the WNT pathway in the signalling hierarchy that drives the onset of gastrulation. This work identifies important molecular mechanisms underlying cell identity transitions during early human embryonic development.