Biomineralization of complex composite architectures comprising the shells of molluscs is known to proceed via self-assembly and in accordance with thermodynamic boundary conditions set by an organic macromolecular framework that is regulated by the organism. Hence, theoretically, the formation of these ultrastructures can be reproduced using the analytical backbone of various physical theories that are commonly employed to express crystal growth of man-made materials. Using a two-dimensional Monte Carlo Potts model simulation, we quantitatively describe and fully predict the structural evolution of the prismatic assembly in the shell of Pinctada nigra. The model, based on hierarchical motion of different types of grain boundaries that are involved in structural formation, has the capacity to describe the morphogenesis of various other biogenic and synthetic polycrystalline composite systems.