Functionalization of metal-organic frameworks (MOFs) with noble metal nanoparticles (NPs) is a challenging task. Conventional impregnation by metals often leads to agglomerates on the surface of MOF crystals. Functional groups on linkers interact with metal precursors and promote the homogeneous distribution of NPs in the pores of MOFs, but their uncontrolled localization can block channels and thus hinder mass transport. To overcome this problem, we created nucleation centers only in the defective pores of the UiO-66 MOF via the postsynthesis exchange. First, we have introduced defects into UiO-66 using benzoic acid as a modulator. Second, the modulator was exchanged for amino-benzoic acid. As a result, amino groups have decorated mainly the defective pores and attracted the Pd precursor after impregnation. The interaction of the metal precursor with amino groups and the growth of NPs were monitored by in situ infrared spectroscopy. Three processes were distinguished: the gaseous HCl release, NH2 reactivation, and growth of extended Pd surfaces. Uniform Pd NPs were located in the pores because of the homogeneous distribution of the precursor and pore diffusion-limited nucleation rate. Our work demonstrates an alternative approach of controlled Pd incorporation into UiO-66 that is of great importance for the rational design of heterogeneous catalysts.