Various cellular activities regulate bone healing, causing structural changes and evolving mechanical characteristics during the regeneration process. This pilot study aimed to correlate the time- and space-resolved mechanical behavior of regenerating and related biological processes. While the mechanical properties of bone are known to be based on a nanostructure organization, this study intends to highlight the evolution of the strain distribution induced by the reconstruction process, which is mainly driven by the mineral part (i.e., hydroxyapatite) of the bone architecture. Multiscale mechanical (tensile and nanoindentation tests) and biological (X-ray microtomography measurements and histological observations) characterization methods were applied to 3 mm rat cranial defects, one of the most reproducible animal models used to assess bone regeneration, filled with bone grafts, the gold standard for bone repair. The size and crystallographic orientation of the hydroxyapatite particles as well as their lattice (elastic) strain distribution under tensile loading were investigated through in situ synchrotron wide-angle and small-angle X-ray scattering measurements at various healing stages. Analyses were completed to quantify the elastic properties at the tissue-scale via nanoindentation measurements. The resulting mappings of lattice strain, mean particle thickness and crystallographic orientations revealed how tissue evolves during bone repair. At the early stages of the regeneration process, the microstructural changes consisted of a restored hydroxyapatite platelet shape and crystallographic orientation. At later stages, the hydroxyapatite crystallographic orientation reached that of native bone, and the mechanical function of the tissue in the defect zone was restored at the mineral particle scale. Nevertheless, even for the longest regeneration duration (20 weeks), mechanical properties at the tissue-scale remained ineffective, highlighting the importance of multiscale investigations to address this type of issue.