Morphogenesis, the process by which cells, tissues, and organs acquire and maintain their form, is essential for embryogenesis, regeneration, and disease progression. During morphogenesis, cells within tissues dynamically interact with biophysical and biochemical signals from their environment by modifying their shape, gene expression, and function. These modifications often lead to transitions between cell states, and with that, to the establishment of functional programs that will in turn define embryonic stages or tissue states. Here, we discuss how the interplay of gene expression programs, chromatin modifications, and biophysical factors from the microenvironment contributes to the robust coordination of morphogenesis by allowing cells within tissues to dynamically transit across functional stages.