Regenerative medicine solutions require thoughtful design to elicit the intended biological response. This includes the biomechanical stimulus to generate an appropriate strain in the scaffold and surrounding tissue to drive cell lineage to the desired tissue. To provide appropriate strain on a local level, new generations of scaffolds often involve anisotropic spatially graded mechanical properties that cannot be characterised with traditional materials testing equipment. Volumetric examination is possible with three-dimensional (3D) imaging, in situ loading and digital volume correlation (DVC). Micro-CT and DVC were utilised in this study on two sizes of 3D-printed inorganic/organic hybrid scaffolds (n = 2 and n = 4) with a repeating homogenous structure intended for cartilage regeneration. Deformation was observed with a spatial resolution of under 200 µm whilst maintaining displacement random errors of 0.97 µm, strain systematic errors of 0.17% and strain random errors of 0.031%. Digital image correlation (DIC) provided an analysis of the external surfaces whilst DVC enabled localised strain concentrations to be examined throughout the full 3D volume. Strain values derived using DVC correlated well against manually calculated ground-truth measurements (R2 = 0.98, n = 8). The technique ensures the full 3D micro-mechanical environment experienced by cells is intimately considered, enabling future studies to further examine scaffold designs for regenerative medicine.