The growing field of MOF-catalyst composites often relies on postsynthetic modifications for the installation of active sites. In the resulting MOFs, the spatial distribution of the inserted catalysts has far-reaching ramifications for the performance of the system and thus needs to be precisely determined. Herein, we report the application of a scanning nuclear microprobe for accurate and nondestructive depth profiling of individual UiO-66 and UiO-67 (UiO = Universitetet i Oslo) single crystals. Initial optimization work using native UiO-66 crystals yielded a microbeam method which avoided beam damage, while subsequent analysis of Zr/Hf mixed-metal UiO-66 crystals demonstrated the potential of the method to obtain high-resolution depth profiles. The microbeam method was further used to analyze the depth distribution of postsynthetically introduced organic moieties, revealing either core-shell or uniform incorporation can be obtained depending on the size of the introduced molecule, as well as the number of carboxylate binding groups. Finally, the spatial distribution of platinum centers that were postsynthetically installed in the bpy binding pockets of UiO-67-bpy (bpy = 5,5'-dicarboxyy-2,2'-bipyridine) was analyzed by microbeam and contextualized. We expect that the method presented herein will be applicable for characterizing a wide variety of MOFs subjected to postsynthetic modifications and provide information crucial for their optimization as functional materials.