Nanocomposites based on isotactic polypropylene/ethylene propylene rubber (iPP/EPR) were prepared adding different amounts of montmorillonite and maleated polypropylene. The structure and morphology of the samples were characterized by small angle X-ray scattering, wide angle X-ray diffraction, electronic and optical microscopy and differential scanning calorimetry, iPP showed a polymorphic behavior. Clay disrupted the ordered crystallization of iPP and had a key role in shaping the distribution of iPP and EPR phases: larger filler contents brought about smaller, less coalesced and more homogeneous rubber domains. Clay distributed itself only in the continuous phase and not in the rubber domains. Tactoids persisted on the surface of the sample, while delamination proceeded to a greater degree in the bulk of the materials. Melt flow rate, impact strength, flexural and tensile properties, were also measured and a structure-property correlation was sought. Clay produced its most significant effect on physical-mechanical properties by controlling the size of rubber domains in the heterophasic matrix. This allowed to obtain nanocomposites with increased stiffness and impact strength, a remarkable achievement for polymer layered-silica nanocomposites that usually suffer the drawback of being stiffer than the unfilled matrix, but at the same time with a lower resistance to impact. A beneficial effect of clay on thermal stability was also observed.