In the present work, a nanocomposite material formed by bacterial cellulose (BC) networks and calcium-deficient hydroxyapatite (HAp) powders was synthesized and characterized. The HAp nanoparticles were previously prepared by a wet chemical precipitation method, starting from aqueous solutions of calcium nitrate and di-ammonium phosphate salts. Energy-dispersive spectroscopy reveals that the prepared HAp corresponds to calcium-deficient hydroxyapatite. BC-HAp nanocomposites were prepared by introducing carboxymethylcellulose (CMC) into the bacteria culture media. HAp nanoparticles were then introduced and remained suspended in the culture medium during the formation of cellulose nanofibrils. The maximum gel thickness was obtained after 21 days of bacteria cultivation. X-ray diffractograms showed the difference of crystallinity among the materials involved in the formation of nanocomposites. The inorganic and organic bonds that corresponded to hydroxyapatite and bacterial cellulose respectively, were depicted by attenuated total reflectance Fourier transform infrared spectra. Scanning electron microscopy and atomic force microscopy measurements confirmed the formation of networks and fibres with smaller diameter corresponding to BC synthesized in the presence of CMC. Image analysis was also used to assess the orientation distributions and Feret diameters for networks of BC and BC-CMC. Thermogravimetric analysis showed that the amount of the mineral phase is 23.7% of the total weight of the nanocomposite. Moreover, HEK cells were cultivated and the biocompatibility of the materials and the cell viability was demonstrated.