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Abstract Oxide heterostructures exhibit a vast variety of unique physical properties. Examples are unconventional superconductivity in layered nickelates and topological polar order in (PbTiO₃)_n/(SrTiO₃)_nsuperlattices. Although it is clear that variations in oxygen content are crucial for the electronic correlation phenomena in oxides, it remains a major challenge to quantify their impact. Here, we measure the chemical composition in multiferroic (LuFeO₃)₉/(LuFe₂O₄)₁superlattices, mapping correlations between the distribution of oxygen vacancies and the electric and magnetic properties. Using atom probe tomography, we observe oxygen vacancies arranging in a layered three-dimensional structure with a local density on the order of 10¹⁴cm⁻², congruent with the formula-unit-thick ferrimagnetic LuFe₂O₄layers. The vacancy order is promoted by the locally reduced formation energy and plays a key role in stabilizing the ferroelectric domains and ferrimagnetism in the LuFeO₃and LuFe₂O₄layers, respectively. The results demonstrate pronounced interactions between oxygen vacancies and the multiferroic order in this system and establish an approach for quantifying the oxygen defects with atomic-scale precision in 3D, giving new opportunities for deterministic defect-enabled property control in oxide heterostructures.