A Cu/ZnO/Al2O3@ZSM-5 core@shell catalyst active for one-step conversion of synthesis gas to dimethyl ether (DME) was imaged simultaneously and in situ using synchrotron-based micro X-ray fluorescence (μ-XRF), X-ray diffraction (μ-XRD), and scanning transmission X-ray microscopy (STXM) computed tomography (CT) with micrometer spatial resolution. An identical sample volume was imaged stepwise, first under oxidizing and reducing atmospheres (imitating calcination and activation processes), and then under model reaction conditions for DME synthesis (H2:CO:CO2 ratio of 16:8:1, up to 250 °C). The multimodal imaging methods offered insights into the active metal structure and speciation within the catalyst, and allowed imaging of both the catalyst core and zeolite shell in a single acquisition. Dispersion of nanosized Cu species was observed in the catalyst core during reduction, with formation of a metastable Cu+ phase at the core-shell interface. Under DME reaction conditions at 1 bar, the coexistence of Cu0 in the active catalyst core together with partially oxidized Cu species was unraveled. The zeolite shell and core-shell interface remained stable under all conditions, preserving the bifunctional nature of the catalyst. These observations are inaccessible using standard bulk techniques like X-ray absorption spectroscopy (XAS) and XRD, demonstrating the potential of multimodal in situ X-ray CT for characterization of hierarchically designed materials, which stand to benefit tremendously from such 3D spatially resolved measurements.