The optimal biomechanical function of the spine depends on hierarchical structures spanning the whole joint to molecular scales. The vertebral endplates experience complex, location specific loading from the intervertebral discs, and their biomechanical behaviour is governed by the microarchitecture, mineralisation, and prestrain of their constituent bone and cartilage. Here we use a combination of synchrotron X-ray tomography, digital volume correlation, and wide-angle X-ray diffraction to investigate relationships between microstructure and mechanics, nanoscale mineral structure, and molecular level prestrain in murine vertebral endplates. Our results show radial variation in endplate structure and local mechanical strain, revealing tensile and shear strains as potential drivers of the cartilage to bone transition. Bone contained narrower mineral crystallites under greater compressive prestrain when compared to calcified cartilage. This multiscale structural adaptation supports load resistance adjacent to the annulus fibrosus and elastic deformation below the nucleus pulposus. Our findings reveal the multiscale mechanics of these mineralised tissues, and the methods presented here have the potential to enhance our understanding of biomechanics in health, disease, and aging.