During gastrulation, embryonic stem cells (ESCs) of the pluripotent epiblast differentiate to form the three embryonic germ lineages and establish the embryonic body-plan. This is a highly spatio-temporally controlled process driven by feedback between different 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 acts to remodel the cellular epigenetic landscape during cell fate choices to direct lineage specification and exit from pluripotency. 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 initial signalling hierarchy that drives the onset of gastrulation. This work identifies important molecular mechanisms underlying cell identity transitions during early human embryonic development.