An objective of this work was to develop novel inorganic–organic nanocomposites based on the hydroxyapatite (HAp) and natural biopolymer ε-polylisine (ε-PL) as bone tissue engineering matrices. For this investigation, the composites with HAp/ε-PL ratios of 50/50 and 70/30 by wt% were prepared through in situ precipitation of HAp in ε-PL aqueous solutions followed by spray drying of obtained suspensions. The FT-IR spectra and FE-SEM micrographs demonstrated that the composites were obtained in a form of spherical microgranules which consist of nanosized apatite crystallites interacted with ε-PL organic phase. The XRD patterns indicated that crystallization behavior of the HAp was affected by addition of ε-PL.