The biomineralization process of nacre and sea-urchin spine occurs under the biological control of specific macromolecules in gelling environments through diverse mechanisms. In both cases, the formation of the crystalline phases – aragonite in nacre and magnesian calcite in sea-urchin spine – takes place through amorphous calcium carbonate precursor phases. Here, these biomineralization processes were investigated by means of counter-diffusion crystallization experiments using agarose highly viscous sols entrapping the soluble organic matrix (SOM) extracted from the two mentioned biominerals. The presence of these SOMs did not increase the supersaturation needed for precipitation, but narrowed the permitted supersaturations with respect to calcium and carbonate ions, when compared to those observed in experiments using synthetic polypeptides or SOM from corals. In the presence of SOMs and diffusing magnesium ions, the analyses of the precipitates suggested that crystallization proceeded through transient amorphous calcium carbonate phases. These favoured the crystallization of aragonite or calcite, according to the biomineral from which SOM was extracted, when a specific concentration was used. This study showed a control of SOMs on the mineralization process, which was more specific for nacre and sea-urchin spine than that for coral skeletons. It also validates the counter-diffusion system as a tool to investigate biomineralization processes in vitro.