Objectives Hydroxyapatite (HAp)/gelatin (GEL) nanocomposite has been developed as a bone substitute. The nanocomposite formation in the GEL matrix is greatly affected by the reaction between Ca 2+ and phosphate ions. The mineralization of GEL macromolecules was investigated through a co-precipitation of calcium phosphates (Ca-P) by using free ions of Ca 2+ and phosphate ions, Pi. The purpose of this study was to prepare a dense HAp/GEL nanocomposite through a free ion production process. Methods Free ionic calcium, Ca 2+, was produced through electrodialysis process using a cation membrane (CMV). Triprotic acid ions were diffused through an anion membrane (AMV) from an aqueous solution of H 3PO 4. The HAp/GEL nanocomposite was prepared by the co-precipitation process. As a reference material for comparison, Ca(OH) 2 and H 3PO 4 were used for the preparation of a HAp/GEL nanocomposite. Results The dense compact body of dried Ca-P/GEL nanocomposite was obtained through the fine chemical reaction of Ca 2+ and Pi. The free calcium ion Ca 2+, diffused from the CMV of the cation reactor greatly affected the formation of Ca–P phase. Phosphate ion species diffused through the AMV in the anion reactor definitely influenced the reaction with Ca 2+. For the formation of the Ca–P phase in the GEL matrix, the organic–inorganic interaction was analyzed using FT-IR. The crystal growth of HAp in the GEL matrix increased with the increase of GEL from XRD, FT-IR and TEM. Significance The mineralization reaction in GEL macromolecules was critically influenced by the free ions of Ca 2+ and inorganic phosphate ions, Pi. The interaction between Ca 2+ and Pi in the GEL matrix was very fine compared to the HAp/GEL nanocomposite prepared from Ca(OH) 2 and H 3PO 4 with the GEL. The dense compact body of HAp/GEL nanocomposite was obtained for an artificial bone application.