We evaluate a method to quantify composition depth gradients in intact metal-organic framework (MOF) single crystals and thereby derive diffusion coefficients of postsynthetically incorporated active sites by nondestructive ion-beam microanalysis. Zr-based UiO-67-bpy (bpy = 2,2'-bipyridine-5,5'-dicarboxylic acid) MOFs were synthesized on Si substrates and then metalated postsynthetically with NiCl2 for 2-48 h, resulting in different Ni depth distributions. Simultaneous micro-Rutherford backscattering spectrometry (μ-RBS) and micro-particle induced X-ray emission (μ-PIXE) analysis were used for the spatially resolved chemical analysis of the MOF single crystals. Qualitative assessment of the μ-RBS spectra indicated the presence of elemental depth gradients and hinted at the governing process of the postsynthetic Ni incorporation, in the present case, molecular diffusion. Quantitative evaluation of the resulting composition depth profiles directly provided the diffusion length and, thereby, the diffusion coefficient of the system. Virtual gradients caused by overhanging tips/edges of the truncated octahedral crystal shape are considered. Furthermore, in the case of insufficient probing depth for μ-RBS, μ-PIXE was still capable of providing qualitative information. In the present system the diffusion coefficient for NiCl2 is found to be (1.72 ± 0.18) × 10-16 m2s-1. The long-term stability of the synthesized and postsynthetically modified MOFs is proved by repeated measurements.