Tin oxide (SnO2) is considered a very promising material as a high capacity Li-ion battery anode. Its adoption depends on a solid understanding of factors that affect electrochemical behavior and performance such as size and composition. We demonstrate here, that defined dispersions and structures can improve our understanding of Li-ion battery anode material architecture on alloying and co-intercalation processes of Lithium with Sn from SnO2 on Si. Two different types of well-defined hierarchical Sn@SnO2 core-shell nanoparticle (NP) dispersions were prepared by molecular beam epitaxy (MBE) on silicon, composed of either amorphous or polycrystalline SnO2 shells. In2O3 and Sn doped In2O3 (ITO) NP dispersions are also demonstrated from MBE NP growth. Lithium alloying with the reduced form of the NPs and co-insertion into the silicon substrate showed reversible charge storage. Through correlation of electrochemical and structural characteristics of the anodes, we detail the link between the composition, areal and volumetric densities, and the effect of electrochemical alloying of Lithium with Sn@SnO2 and related NPs on their structure and, importantly, their dispersion on the electrode. The dispersion also dictates the degree of co-insertion into the Si current collector, which can act as a buffer. The compositional and structural engineering of SnO2 and related materials using highly defined MBE growth as model system allows a detailed examination of the influence of material dispersion or nanoarchitecture on the electrochemical performance of active electrodes and materials.