This work provides a detailed study on the physico-chemical characterization of a mechanized silver–gold alloy@mesoporous silica shell/pseudorotaxane nano-assembly using two main complementary techniques: XPS and NMR (liquid- and solid-state). The pseudorotaxane nanovalve is composed of a stalk (N-(6-aminohexyl)-aminomethyltriethoxysilane)/macrocycle (cucurbit[6]uril (CB6)) complex anchored to the silica shell leading to a silica/nanovalve hybrid organic–inorganic interface that has been fully characterized. The stalk introduction in the silica network was clearly demonstrated by XPS measurements, with the Si 2p peak shifting to lower energy after grafting, and through the analysis of the C 1s and N 1s core peaks, which indicated the presence of CB6 on the nanoparticle surface. For the first time, the complex formation on nanoparticles was proved by high speed 1H MAS NMR experiments. However, these solid state NMR analyses have shown that the majority of the stalk does not interact with the CB6 macrocycle when formulated in powder after removing the solvent. This can be related to the large number of possible organizations and interactions between the stalk, the CB6 and the silica surface. These results highlight the importance of using a combination of adapted and complementary highly sensitive surface and volume characterization techniques to design tailor-made hybrid hierarchical structured nano-assemblies with controlled and efficient properties for potential biological purposes.