The structure of poly(organosiloxane) nanocapsules partially filled with iron oxide cores of different sizes was revealed by small angle X-ray scattering and X-ray diffraction. The nanocapsules are synthesized by the formation of a poly(organosiloxane) shell around iron oxide nanoparticles and the simultaneous partial dissolution of these cores. Due to the high scattering contrast of the iron oxide cores compared to the polymer shell, the particle size distribution of the cores inside the capsules can be measured by small angle X-ray scattering. Additional information can be revealed by X-ray diffraction, which gives insights into the formation of the polymer network and the structure of the iron oxide cores. The study shows how the crystallinity and size of the nanoparticles as well as the shape and width of the size distribution can be altered by the synthesis parameters.