Mollusk shell is one of the best studied of all calcium carbonate biominerals. Its silk-like binder-matrix protein plays a pivotal role during the formation of aragonite crystals in the nacre sheets. Here, we provide novel experimental insights into the interaction of mineral and protein compounds using a model system of reconstituted Bombyx mori silk fibroin solutions serving as templates for the crystallization of calcium carbonate (CaCO3). We observed that the inherent (self-assembling) aggregation process of silk fibroin molecules affected both the morphology and crystallographic polymorph of CaCO3 aggregates. This combination fostered the growth of a novel, rice-grain-shaped protein/mineral hybrid with a hollow structure with an aragonite polymorph formed after ripening. Our observations suggest new hypotheses about the role of silk-like protein in the natural biomineralization process, but it may also serve to shed light on the formation process of those ‘ersatz’ hybrids regulated by artificially selected structural proteins.