In 2007 Shinya Yamanaka demonstrated that human fibroblasts can be reverted back to a pluripotent state by the forced expression of the four transcription factors; OCT4, SOX2, KLF4 and cMYC. These so-called induced pluripotent stem cells (iPSCs), like embryonic stem cells derived from the epiblast of blastocysts, can give rise to any cell type of the body. Furthermore, iPSCs carry the promise of personalised regenerative medicine and hold tremendous potential for applications such as cell replacement therapies, disease modelling and in vitro drug screening. However, the molecular mechanisms of these cellular transitions into primed or naive human-induced pluripotency remain poorly understood. To address this, we reconstructed the molecular reprogramming trajectories using single cell transcriptomics. This revealed that reprogramming into the primed and naive human pluripotency states follows diverging and distinct trajectories. The integration of regulatory element usage with transcriptomics unveiled an unexpected role of trophectoderm (TE) lineage-associated transcription factors, as well as a subpopulation of cells that transiently upregulated a TE-like signature during reprogramming. We demonstrated that this TE state could be stabilised allowing the derivation of induced Trophoblast Stem Cells (iTSCs). Further inspection of these cell cultures also revealed the upregulation of a primitive endoderm-like signature in some of the cells. Unexpectedly, when all these cells are allowed to contact each other in a 3-dimensional system, they self-organise giving rise to blastocyst-like structures which we termed, iBlastoids. iBlastoids are capable of modelling in vitro, many molecular, morphological and functional aspects of embryonic development during the early stages of implantation.