The synthesis, morphology and luminescence properties of two systems comprising luminescent Eu3+-doped zirconium oxide nanocrystals embedded in an amorphous silica matrix are reported. The two systems, prepared with the same overall wt% composition of silica (75%) and EuxZr(1−x)O(2−x/2) solid solution (25%), have been annealed in the range 135–1000 °C and subsequently functionalized with (3-aminopropyl)triethoxysilane. Detailed X-ray diffraction analyses and transmission electron micrographs, combined with infrared spectroscopy and luminescence spectroscopy data, have been used to demonstrate the influence of annealing temperature on the: (i) nanostructure, (ii) luminescence properties and (iii) availability of superficial –OH groups for efficient surface functionalization. The optimum calcination temperature was found to be 700 °C for each series in terms of luminescence lifetime efficiency and post-functionalization efficiency with (3-aminopropyl)triethoxysilane.