Animal embryo-like fossils from the Ediacaran Doushantuo Formation, South China, have been interpreted as the earliest metazoan fossils, significantly predating the radiation of biomineralizing animals and macroscopic bilaterians during the Ediacaran–Cambrian transition. The exceptional cellular and intracellular preservation of the Doushantuo fossils can provide tantalizing glimpses into the organellic structures of these multicellular eukaryotes. The organelle-like features are distinguishable in light, electron, and X-ray imaging, a distinction that has been assumed to be a result of compositional variation. Combined electron microscopic and X-ray tomographic analyses, however, reveal that crystalline textural variation may also contribute to the visibility of these intracellular structures. Specifically, cell lumina and lipid vesicle-like (or yolk granule-like) structures are preserved as nanometer-sized, randomly oriented apatite crystals, whereas cell boundaries and nucleus-like structures are preserved as botryoidal aggregates of micrometer-sized apatite crystals. These textural differences render contrast in electron and X-ray imaging, and they also indicate two mineralization stages, with the botryoidal aggregates at the cell boundaries and nucleus-like structures representing late-stage overgrowth or void-filling cementation. These findings suggest that, while the Doushantuo intracellular structures may occupy the same topological position as strongly degraded nuclei and vesicles, they do not represent organelles with intact enclosing membranes. Instead, the membrane-like structures that characterize the nucleus-like structures are mostly late-stage cements, critically undermining recent hypotheses about the nature of nuclear division and the non-animal holozoan affinity of the Doushantuo fossils, which assume a biological origin of such membrane-like structures.