It is a major outstanding goal in nanotechnology to precisely position functional nanoparticles, such as quantum dots, inside a three-dimensional (3D) nanostructure in order to realize innovative functions. Once the 3D positioning is performed, the challenge arises how to nondestructively verify where the nanoparticles reside in the 3D nanostructure. Here, we study 3D photonic band gap crystals made of Si that are infiltrated with PbS nanocrystal quantum dots. The nanocrystals are covalently bonded to polymer brush layers that are grafted to the Si–air interfaces inside the 3D nanostructure using surface-initiated atom transfer radical polymerization (SI-ATRP). The functionalized 3D nanostructures are probed by synchrotron X-ray fluorescence (SXRF) tomography that is performed at 17 keV photon energy to obtain large penetration depths and efficient excitation of the elements of interest. Spatial projection maps were obtained followed by tomographic reconstruction to obtain the 3D atom density distribution with 50 nm voxel size for all chemical elements probed: Cl, Cr, Cu, Ga, Br, and Pb. The quantum dots are found to be positioned inside the 3D nanostructure, and their positions correlate with the positions of elements characteristic of the polymer brush layer and the ATRP initiator. We conclude that X-ray fluorescence tomography is very well suited to nondestructively characterize 3D nanomaterials with photonic and other functionalities.