Biphasic calcium phosphate/poly-L-lactide granules of 150–200 μm sizes were subjected to high-energy mechanical milling in a planetary ball mill for up to 480 minutes. Characterization of the material obtained was carried out using X-ray diffraction (XRD), differential scanning calorimetry (DSC), environmentally scanning electronic microscopy (ESEM), transmission electron microscopy (TEM) and infrared spectroscopy (IR). These techniques confirmed that mechanical milling induced significant changes in the biocomposite structure and properties. The most significant changes are reduction of the HAp crystallites size from 99.8 to 26.7 nm and β-TCP from 97.3 to 29.6, as well as crystallinity of PLLA phases. Homogeneous phase distribution (arrangement) is obtained by extending the duration of mechanical milling.