In this Paper, $$\hbox {YCa}_{2}\hbox {Cu}_{3}\hbox {O}_{7}$$ superconductor composites were fabricated with biocompatible carbonate calcium nanoparticles. The effect of the biocompatible nanoparticle on YBCO superconductor properties were investigated. For this purpose, planetary ball milling process used to produce $$\hbox {CaCO}_{3}$$ nanoparticles from cuttlebone (Sepia pharaonis) of the Persian Gulf. Then, samples of superconductor composite with the natural carbonate calcium were fabricated. The samples were prepared by solid state reaction method with mixing, calcination and sintering process. The samples were characterized and studied using dynamic light scattering technique, Meissner effect test, XRD analysis and FESEM imaging. The critical current density ($$J_\mathrm{C}$$) and oxygen content of samples were measured by traditional four-probes method and iodometric titration method, respectively. The superconducting transition temperatures and $$J_\mathrm{C}$$ were determined 90.2 K and 28.4 $$\hbox {A}/\hbox {cm}^{2}$$ by four-probe method measurements, respectively. The results showed a significant enhancement of the superconducting $$J_\mathrm{C}$$ due to using the natural $$\hbox {CaCO}_{3}$$ nanoparticles in the samples.