In vitro cultured stem cells with distinct developmental capacities can contribute to embryonic or extraembryonic tissues after microinjection into pre-implantation mammalian embryos. However, whether cultured stem cells can independently give rise to entire gastrulating embryo-like structures with embryonic and extraembryonic compartments remains unknown. Here, we adapt a recently established platform for prolonged ex utero growth of natural embryos to generate mouse post-gastrulation synthetic whole embryo models (sEmbryos), with both embryonic and extraembryonic compartments, starting solely from naive ESCs. This was achieved by co-aggregating non-transduced ESCs, with naive ESCs transiently expressing Cdx2 or Gata4 to promote their priming toward trophectoderm and primitive endoderm lineages, respectively. sEmbryos adequately accomplish gastrulation, advance through key developmental milestones, and develop organ progenitors within complex extraembryonic compartments similar to E8.5 stage mouse embryos. Our findings highlight the plastic potential of naive pluripotent cells to self-organize and functionally reconstitute and model the entire mammalian embryo beyond gastrulation. Display omitted •Advanced synthetic embryos (sEmbryos) self-assembled from ESCs in an ex utero setup•Naive ESCs give rise to all embryonic and extraembryonic compartments in sEmbryos•Post-gastrulation stem cell derived sEmbryos develop organ-specific progenitors•Extraembryonic compartments adequately develop in post-gastrulation whole sEmbryos Post-gastrulation stages of development with organ progenitors and complex extra-embryonic compartments are achieved ex utero entirely from assembled naive mouse embryonic stem cells.