The polymer layer-by-layer assembly is accounted among the most attractive approaches for the design of advanced drug delivery platforms and biomimetic materials in 2D and 3D. The multilayer capsules can be made of synthetic or biologically relevant ( e.g. , natural) polymers. The biopolymers are advantageous for bioapplications; however, the design of such “biocapsules” is more challengeable due to intrinsic complexity and lability of biopolymers. Until now, there are no systematic studies that report the formation mechanism for multilayer biocapsules templated upon CaCO 3 crystals. This work evaluates the structure–property relationship for 16 types of capsules made of different biopolymers and proposes the capsule formation mechanism. The capsules have been fabricated upon mesoporous cores of vaterite CaCO 3 , which served as a sacrificial template. Stable capsules of polycations poly- l -lysine or protamine and four different polyanions were successfully formed. However, capsules made using the polycation collagen and dextran amine underwent dissolution. Formation of the capsules has been correlated with the stability of the respective polyelectrolyte complexes at increased ionic strength. All formed capsules shrink upon core dissolution and the degree of shrinkage increased in the series of polyanions: heparin sulfate < dextran sulfate < chondroitin sulfate < hyaluronic acid. The same trend is observed for capsule adhesiveness to the glass surface, which correlates with the decrease in polymer charge density. The biopolymer length and charge density govern the capsule stability and internal structure; all formed biocapsules are of a matrix-type, other words are microgels. These findings can be translated to other biopolymers to predict biocapsule properties.