The metal-organic framework MOF-808 contains Zr6O8 nodes with a high density of vacancy sites, which can incorporate carboxylate-containing functional groups to tune chemical reactivity. Although the postsynthetic methods to modify the chemistry of the Zr6O8 nodes in MOFs are well known, tackling these alterations from a structural perspective is still a challenge. We have combined infrared spectroscopy experiments and first-principles calculations to identify the presence of node vacancies accessible for chemical modifications within the MOF-808. We demonstrate the potential of our approach to assess the decoration of MOF-808 nodes with different catechol–benzoate ligands. Furthermore, we have applied advanced synchrotron characterization tools, such as pair distribution function analyses and X-ray absorption spectroscopy, to resolve the atomic structure of single metal sites incorporated into the catechol groups postsynthetically. Finally, we demonstrate the catalytic activity of these MOF-808 materials decorated with single copper sites for 1,3-dipolar cycloadditions.