Developing new methods to prepare pseudocapacitive materials with high pseudocapacitance/electronic conductivity is of great interest for hybrid supercapacitors. Recently, the exfoliation/restacking of manganese and cobalt layered transition metal oxides was proposed. Despite improved electrochemical performance of such Mn-Co composites, their bulk organization (i.e. the scale at which the stacking occurs) and structure (i.e. porosity…) remains to be elucidated so far. To tackle this issue, here, SEM and Auger analysis with a nanoscale resolution, coupled to cross-section preparation is proposed. A good correlation between the restacking method, the nanoscale organization/structure of composites and resulting electrochemical performance is obtained. Importantly, the combination of cross-section with Auger analysis allows revealing the nanoscale stacking of the Mn and Co phases. Also, the porosity of the nano-composites, revealed by the cross-section preparation, is correlated to the speed of the restacking process. A fast flocculation step forms aggregates with a porous bulk structure while a slow flocculation step leads to a dense and closed bulk structure of the aggregates. These results highlight that a better control/understanding of the organization/structure of such nanocomposites can lead to further improvement. Overall, the innovative cross-section Auger approach proposed in this study should also benefit to the understanding of other nano-composites.