Deciphering molecular events underlying human embryo development during the peri-implantation window is essential to improve medically assisted reproduction. Here, we present a biologically curated transcriptomic atlas of human embryos spanning days 3 to 14 post-fertilization (d.p.f.). Through weighted gene co-expression network analysis, we identified lineage-specific gene modules and revealed markers of a progressive acquisition of cell identities. We uncovered transcription factors acquired during the naïve-to-primed transition in human embryos and blastoids. We characterized transcriptional regulators of the trophoblast lineage, and inferred the upstream gene regulatory network using SCENIC, identifying putative drivers of polar maturation. Using proteomic and immunofluorescence data, we substantiated the developmental stage of stem cell models and linked human trophoblast stem cells to 8 d.p.f. trophoblast. Lastly, we staged two blastoid models, demonstrating that they adequately unroll key molecular milestones of pre- to post-implantation embryos.