We introduce a new approach to defect engineering in Zr-based metal-organic frameworks (Zr-MOFs), aiming to reduce Zr site valency while preserving high node connectivity. Using a rapid heat treatment (RHT) in humid air, oxygen vacancies (O-vacancies) were created in Dresden University of Technology (DUT)-67 through cluster dehydration. Unlike conventional defect engineering, aimed at creating missing-linker defects, this method breaks intra-cluster Zr-μ3O–Zr bonds, generating coordinatively unsaturated Zr (Zrcus) sites. Pair distribution function (PDF) analysis, X-ray absorption spectroscopy (XAS), and density functional theory (DFT) calculations reveal that the O-vacancies lead to symmetry breaking, irreversible node distortions, and framework amorphization. This treatment converts 50% of metal sites to Zrcus sites, nearly doubling the catalytic activity of DUT-67 in glyoxal conversion to glycolic acid. DFT modeling and in situ PDF analysis highlight the dynamic behavior of Zr clusters under reaction conditions, suggesting a new avenue for defect engineering in Zr-MOFs to enhance catalytic performance.