We revisit the ultrastructural features of different calcareous biominerals and identify remarkable similarities: taxonomically very distant species show a common nanogranular structure, even if different extracellular secretion patterns are employed or calcium carbonate polymorphs formed. By these analyses, we elucidate the locus of the small fraction of intracrystalline organic matrix revealing its intergranular character and localize the intracrystalline amorphous calcium carbonate moiety commonly found in mesocrystalline biominerals and provide a first explanation for the pathway by which it is preserved.