We present an approach for multi-layer preparation to perform microstructure analysis of a Li-ion cell anode active material using synchrotron tomography. All necessary steps, from the disassembly of differently-housed cells (pouch and cylindrical), via selection of interesting layer regions, to the separation of the graphite-compound and current collector, are described in detail. The proposed stacking method improves the efficiency of synchrotron tomography by measuring up to ten layers in parallel, without the loss of image resolution nor quality, resulting in a maximization of acquired data. Additionally, we perform an analysis of the obtained 3D volumes by calculating microstructural characteristics, like porosity, tortuosity and specific surface area. Due to a large amount of measurable layers within one stacked sample, differences between aged and pristine material (e.g., significant differences in tortuosity and specific surface area, while porosity remains constant), as well as the homogeneity of the material within one cell could be recognized.