The structure of matter at the nanoscale, in particular that of amorphous metallic alloys, is of vital importance for functionalization. With the availability of synchrotron radiation, it is now possible to visualize the internal features of metallic samples without physically destroying them. Methods based on computed tomography have recently been employed to explore the local features. Tomographic reconstruction, while it is relatively uncomplicated for crystalline materials, may generate undesired artifacts when applied to featureless amorphous or nanostructured metallic alloys. In this study we show that X-ray diffraction computed nanotomography can provide accurate details of the internal structure of a metallic glass. We demonstrate the power of the method by applying it to a hierarchically phase-separated amorphous sample with a small volume fraction of crystalline inclusions, focusing the X-ray beam to 500 nm and ensuring a sub-micrometer 2D resolution via the number of scans.