In this work, we report the results of a detailed structural study of a promising bioceramic material silicocarnotite Ca5(PO4)2SiO4 (SC) synthesized from mechanochemically treated nanosized silicon-substituted hydroxyapatite by annealing at 1000 °C. This novel synthetic approach represents an attractive and efficient route towards large-scale manufacturing of the silicocarnotite-based bioceramics. A combination of solid-state nuclear magnetic resonance (NMR), powder X-ray crystallography and density function theory (DFT) calculations has been implemented to characterize the phase composition of the prepared composite materials and to gain insight into the crystal structure of silicocarnotite. The phase composition analysis based on the multinuclear solid-state NMR has been found in agreement with X-ray powder diffraction indicating the minority phases of CaO (5–6 wt%) and residual silicon-apatite (7–8 wt%), while the rest of the material being a fairly crystalline silicocarnotite phase (86–88 wt%). A combination of computational (CASTEP) and experimental methods was used to address the anionic site disorder in the silicocarnotite crystal structure. Distorted [OPO3] pyramids have appeared as an important structural motif in the SC crystal structure. The ratio between regular [PO4] and distorted [OPO3] tetrahedra is found between 2:1 and 3:1 based on XRD experiments and CASTEP calculations. The natural abundance 43Ca magic angle spinning NMR spectra of silicocarnotite are reported for the first time.