Defect engineering can enhance key properties of metal-organic frameworks (MOFs). Tailoring the distribution of defects, for example in correlated nanodomains, requires characterization across length scales. However, a critical nanoscale characterization gap has emerged between the bulk diffraction techniques used to detect defect nanodomains and the sub-nanometer imaging used to observe individual defects. Here, we demonstrate that the emerging technique of scanning electron diffraction (SED) can bridge this gap uniquely enabling both nanoscale crystallographic analysis and the lowdose formation of multiple diffraction contrast images for defect analysis in MOFs. We directly image defect nanodomains in the MOF UiO-66(Hf) over an area of ca. 1 000 nm and with a spatial resolution ca. 5 nm to reveal domain morphology and distribution. Based on these observations, we suggest possible crystal growth processes underpinning synthetic control of defect nanodomains. We also identify likely dislocations and small angle grain boundaries, illustrating that SED could be a key technique in developing the potential for engineering the distribution of defects, or “microstructure”, in functional MOF design.