Biogenic single-crystal composites, such as sea urchin spines and calcitic prisms from mollusk shells, contain organic macromolecules inside of inorganic single-crystal matrices. The nanoscale internal structure of these materials, however, is poorly understood, especially how the biomacromolecules are distributed within the crystals without significantly disrupting the crystalline lattice. Here, annular dark-field scanning transmission electron microscopy and electron tomography reveal, in three dimensions, how biomacromolecules are distributed within the calcitic prisms from Atrina rigida shells. Disk-like nanopatches, whose scattering intensity is consistent with organic inclusions, are observed to be anisotropically arranged within a continuous, single-crystalline calcite matrix. These nanopatches are preferentially aligned with the (000l) planes of calcite. Along the crystallographic c-axis, there are alternating organic-rich and -poor regions on a length scale of tens of nanometers, while, in the ab plane, the distribution of nanopatches is more random and uniform. The structural features elucidated in this work have relevance to understanding the structure-property relationships and formation mechanisms of biominerals, as well as to the development of bio-inspired strategies to extrinsically tune the properties of single-crystals.