Composite materials based on gels and hydroxyapatite could provide promising characteristics for biomedical materials because of biocompatibility, osteointegration, and easy implementation. In this research, enzymatic synthesis of hydroxyapatite was studied as a technique for tissue engineering and scaffolds creation. The hydroxyapatite crystals were synthesized using this method and characterized with X-ray diffraction, electron microscopy, IR and Raman spectroscopy and analytical methods. As a result, a material with assumed composition of Ca10−x(HPO4)x(PO4)6−x(OH)2−x/CaHPO4/CaCO3 was obtained by enzymatic synthesis. The dynamics of size evolution, texture and crystallinity of the solid phase as a function of deposition time were also investigated. Afterwards, this method was used for gel mineralization with hydrogels such as agarose, alginate, gelatin, and polyacrylamide. Hydroxyapatite crystals obtained inside and above the hydrogels were analyzed with X-ray diffraction and electron microscopy. The particle diameter distribution functions were used to evaluate the mineralization in different gels. The shape and size of mineral inclusions depend on the density of the hydrogel grid. The localization of the formed solid phase depends on the nature of the gel and the concentration of alkaline phosphatase inside it. The results provide an opportunity to control the morphology of calcium phosphate particles produced during mineralization, which is important for the creation of biomedical materials with specified and reproducible characteristics.