Nanocomposites have great potential for the rational synthesis of tailored materials. However, the templating process that transfers the self-organized nanostructure of a block copolymer or other mesophase onto the functional material is by no means trivial, and often involves multiple steps, each of which presents its own chemical and physical challenges. As a result the nanocomposite may not be homogeneous, but can be phase-separated into various components which may feature their own specific microstructure. Here it is shown how scanning microbeam small-angle X-ray scattering (µSAXS) can be used to characterize a thermoset resol/poly(isoprene-block-ethylene oxide) nanocomposite on multiple length scales with respect to homogeneity and microphase separation.