Reprogramming of somatic cells in defined conditions can give rise to primed and naive human induced pluripotent stem cells (hiPSCs) that recapitulate pre-implantation and post-implantation epiblasts respectively. However, the molecular events underpinning these processes are largely unexplored, impeding further rational optimisation of the reprogramming protocols. In this study, we reconstruct high-resolution molecular roadmaps of primed and naive human reprogramming at the single-cell level, and show distinct and independent cell fate transitions along each of the reprogramming trajectories. This revealed that reprogramming into primed and naive human pluripotency initially follows a shared trajectory before bifurcating into the two distinct pluripotent states, with neither states requiring a transition through the other. By extracting cell surface marker profiles of intermediate populations during the cellular transitions, we isolated and profiled reprogramming intermediates under several other naive as well as extended pluripotent conditions throughout reprogramming. We find each of them follow either of the bifurcated trajectories. Furthermore, using the same isolation strategy, we profiled genome-wide chromatin accessibility of reprogramming intermediates uncovering both individual intronic regulatory elements in core pluripotency markers, as-well-as a global association of increased chromatin accessibility with trophectoderm (TE) and epiblast (EPI) lineage-related transcription factors during the divergence into naive human pluripotency. Taken together, our comprehensive analyses of human primed and naive reprogramming reveal a remarkable and unexpected role of the TE-lineage associated regulatory program play during this process, providing novel insights to study early human lineage specification.