Aqueous dispersions of semiconducting nanoparticles have shown promise as a robust and scalable platform for the production of efficient polymer/fullerene active layers in organic photovoltaic applications. Semiconducting nanoparticles are a composite of both an n-type and p-type semiconductor contained within a single nanoparticle. In order to realize efficient organic solar cells from these materials, there is a need to understand how the size and internal distribution of materials within each nanoparticle contributes to photocurrent generation in a nanoparticle-derived device. Therefore, characterizing the internal distribution of conjugated polymer and fullerene within the dispersion is the first step to improving performance. To date, study of polymer/fullerene structure within these nanoparticles has been limited to microscopy techniques of deposited nanoparticles. In this work, we use contrast variation with small-angle neutron scattering to determine the internal distribution of poly(3-hexylthiophene) and [6,6]phenyl-C61-butyric acid methyl ester inside the composite nanoparticles as a function of formulation while in dispersion. On the basis of these measurements, we connect the formulation of these nanoparticles with their internal structure. Using electrostatic deposited monolayers of these nanoparticles, we characterize intrinsic charge generation using photoconductive atomic force microscopy and correlate this with structures determined from small-angle neutron scattering measurements. These techniques combined show that the best performing composite nanoparticles are those that have a uniform distribution of conjugated polymer and fullerene throughout the nanoparticle volume such that electrons and holes are easily transported out of the particle.