Understanding how the nanostructured materials evolve and interact inside real operating devices is essential to optimize their performance. Of the various techniques developed that provide insight into such designer materials and devices, those based on diffraction are particularly useful. However, to date, these have been heavily restrictive, providing information only on materials that exhibit high crystallographic ordering and idealized samples of isolated components, not as they function in operating devices. This methods combines X-ray atomic pair distribution function analysis and computed tomography to overcome this limitation. It allows the structure of nanocrystalline and amorphous materials to be identified, quantified and their structure spatially mapped with micron-scale resolution. We applied this method to different systems such as industrial Pd/PdO catalyst and batteries. The method will have impact across a range of disciplines from materials science, biomaterials, geology, environmental science, palaeontology and cultural heritage to health.