The performance of functional materials is either driven or limited by nanoscopic heterogeneities distributed throughout the material’s volume. To better our understanding of these materials, we need characterization tools that allow us to determine the nature and distribution of these heterogeneities in their native geometry in 3D. Here, we introduce a method based on x-ray near-edge spectroscopy, ptychographic x-ray computed nanotomography, and sparsity techniques. The method allows the acquisition of quantitative multimodal tomograms of representative sample volumes at sub–30 nm half-period spatial resolution within practical acquisition times, which enables local structure refinements in complex geometries. To demonstrate the method’s capabilities, we investigated the transformation of vanadium phosphorus oxide catalysts with industrial use. We observe changes from the micrometer to the atomic level and the formation of a location-specific defect so far only theorized. These results led to a reevaluation of these catalysts used in the production of plastics.