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The integration of layer-by-layer (LbL) and self-assembly methods has the potential to achieve precision assembly of nanocomposite materials. Knowledge of how nanoparticles move across and within stacked materials is critical for directing nanoparticle assembly. Here, we investigate nanoparticle self-assembly within two different LbL architectures: (1) a bilayer composed of two immiscible polymer thin-films, and (2) a bilayer composed of polymer and graphene that possesses a “hard-soft” interface. Polymer-grafted silver nanocubes (AgNCs) are employed as a model nanoparticle system for systematic experiments – characterizing both assembly rate and resulting morphologies – that examine how assembly is affected by the presence of an interface. We observe that polymer grafts can serve to anchor AgNCs at the bilayer interface and to decrease particle mobility, or can promote particle transfer between layers. We also find that polymer viscosity and polymer mixing parameters can be used as predictors of assembly rate and behavior. These results provide a pathway for designing more complex multilayered nanocomposites.