We investigated the interaction of natural derived macromolecular multilayers with calcium and phosphate ions entirely processed using the layer-by-layer (LbL) technique. A nanostructured multilayer component, with 5 or 10 bilayers, was first produced using weak polyelectrolyte biopolymers, chitosan and chondroitin sulfate. This was followed by sequential passing of solutions containing Ca2+ and PO43− over the multilayers. QCM-D, SEM and EDX results conferred the formation of calcium phosphate (CaP) over the polyelectrolyte multilayers. Initiation of precipitation was observed earlier in the 10 bilayers coating than in the 5 bilayers one. These results indicate the potential of multilayers to trap ions, as a biomimetic approach that can be used to induce CaP precipitation. This could enable the preparation of more performant bioactive composite biomaterials for orthopedic applications, including in bone tissue engineering.