It has been proposed that the intrinsic property of nucleosome arrays to undergo liquid-liquid phase separation (LLPS) in vitro is responsible for chromatin domain organization in vivo. However, understanding nucleosomal LLPS has been hindered by the challenge to characterize the structure of the resulting heterogeneous condensates. We used cryo-electron tomography and deep-learning-based 3D reconstruction/segmentation to determine the molecular organization of condensates at various stages of LLPS. We show that nucleosomal LLPS involves a two-step process: a spinodal decomposition process yielding irregular condensates, followed by their unfavorable conversion into more compact, spherical nuclei that grow into larger spherical aggregates through accretion of spinodal materials or by fusion with other spherical condensates. Histone H1 catalyzes more than 10-fold the spinodal-to-spherical conversion. We propose that this transition involves exposure of nucleosome hydrophobic surfaces causing modified inter-nucleosome interactions. These results suggest a physical mechanism by which chromatin may transition from interphase to metaphase structures. [Display omitted] • Tetranucleosome phase separation involves a two-step condensation process • Spinodal decomposition causes the initial formation of loosely packed irregular condensates • Nuclei formation within spinodal condensates gives raise to denser spherical condensates • Histone H1 catalyzes more than 10-fold the spinodal-to-spherical condensate conversion Zhang et al. demonstrate that liquid-liquid phase separation of tetranucleosome arrays occurs in two steps: a spinodal decomposition involving formation of loosely arranged irregular condensates, followed by the emergence of tightly packed spherical nuclei. The structure of nucleosome condensates by cryo-ET suggests a physical mechanism of chromatin compaction in vivo. [ABSTRACT FROM AUTHOR]