The function of all musculoskeletal joints depends on hierarchical structures spanning the molecular to whole joint scales. Investigating biomechanics across length scales requires correlative multiscale experimental methods. This study applies multimodal in situ synchrotron imaging techniques to spinal joints, focussing on the vertebral endplates, to explore relationships between structure and mechanical strain across spatial scales. Strain mapping using digital volume correlation combined with microarchitectural analysis reveals that high tensile and shear strains play a role in the cartilage to bone transition. Correlative imaging and diffraction show that bone contains narrower mineral nano-crystallites under greater compressive prestrain compared to calcified cartilage. We hypothesise that this multiscale structural adaptation supports the mechanical function of the intervertebral disc. Future applications of the techniques presented here have potential to help unravel biomechanical underpinnings of pathologies affecting mineralised tissue structure. The multiscale structure-function relationships uncovered here may inspire the design of biomaterials and orthopaedic implants.