Here introduced a route for the synthesis of 3D structures that display a mechanical strength that competes with that of the toughest materials found in nature. Following the “brick-and-mortar” biomineralization typical of nacre, self-stratified, periodic materials are obtained by one-step ion diffusion gradient and hydrogelation of nanochitin with simultaneous mineral coprecipitation. Specifically, under appropriate electrolyte conditions, hydroxyapatite (HA) microspheres grow in an organic network formed from partially deacetylated chitin nanofibers (NCh), resulting in periodic stacking of mineralized (HA) and non-mineralized (NCh) layers. By directional diffusion, customizable 3D shapes are self-assembled and demonstrated to function as optical waveguides with selective light transmission at interfaces. Upon hot pressing, the resulting solid structures exhibit a superb mechanical performance while being biocompatible (tested with chondrogenic ATDC5 cells as a model for physiological mineralization). Overall, a shape-controlled, one-pot biomineralization method was proposed that achieves hierarchical, periodic and strong “nacre-like” structures suitable as biomedical material.