Deformation mechanisms in bone matrix at the nanoscale control its exceptional mechanical properties, but the detailed nature of these processes is as yet unknown. In situ tensile testing with synchrotron X-ray scattering allowed us to study directly and quantitatively the deformation mechanisms at the nanometer level. We find that bone deformation is not homogeneous but distributed between a tensile deformation of the fibrils and a shearing in the interfibrillar matrix between them.