An emerging theme of modern composites and devices is the coupling of nanostructural properties of materials with their targeted arrangement at the microscale. Of the imaging 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. Here we describe a method that uses a combination of 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 mapped. We demonstrate the method with a phantom object and subsequently apply it to resolving, in situ, the physicochemical states of a heterogeneous catalyst system. The method may have potential impact across a range of disciplines from materials science, biomaterials, geology, environmental science, palaeontology and cultural heritage to health.