The structure of the multilayer assemblies of yttrium iron garnet nanoparticles (YIG) with polyelectrolytes was investigated with the emphasis on the control of the particle density in the adsorption layers. It was found that the growth of YIG films prepared by the layer-by-layer assembly can occur via two deposition modes: (1) sequential adsorption of densely packed adsorption layers (normal growth mode) and (2) in-plane growth of isolated particle domains (lateral expansion mode). Importantly, the dependence of the optical density on the number of deposition cycles remains linear in both cases. Microscopy results indicate that the origin of the lateral growth is in the interplay of particle/particle and particle/polyelectrolyte interactions rather than in a substrate effect. The lateral expansion mode is a general attribute of the layer-by-layer deposition and can be observed for various aqueous colloids. For the preparation of sophisticated multifunctional assemblies on nanoparticles, the film growth via domain expansion should be avoided, and therefore, one must be able to control the growth pattern. The switch from lateral to normal growth mode can be effected by grafting charged organic groups to YIG nanoparticles. Hydrophobic interactions between the hydrocarbon groups of the modified YIG and polyelectrolyte significantly increase the attractive component of the particle/polyelectrolyte and particle/particle interactions. The films from modified YIG display densely packed nanoparticle layers with a greatly reduced number of defects.