The coating of nuclear fuel kernels with pyrolytic carbon (PyC) is a well-understood practice dating back over half a century. In spite of decades of studies related to these coatings, no study has yet investigated the effect of the PyC deposition coating process on the kernels themselves. In this study, the composition and crystallographic phase of kernel materials were observed to change after exposure to the thermal and chemical environment of the PyC coating process. Specifically, the coating process increased the fraction of high carbon content phase within carbide microsphere kernels, with W2C containing microspheres driven toward WC, and UC containing microspheres driven toward UC2. Oxide microspheres consisted of a mixture of two crystalline phases. The monoclinic phase within yttria-stabilized zirconia microspheres was eliminated by the coating process resulting in a purely tetragonal phase. Hafnium oxide microspheres were more stable showing no detectable change in composition or crystal structure after coating.