Zirconium-based metal–organic frameworks (Zr-MOFs) are a subclass of MOFs known for their remarkable stability, especially in the presence of water. This makes them extremely attractive for practical applications, including CO₂ capture from industrial emission sources; however, the CO₂ adsorption capacity of Zr-MOFs is moderate compared to that of the best performing MOFs reported to date. Functionalization of Zr-MOFs with amino groups has been demonstrated to increase their affinity for CO₂. In this work, we assessed the potential of post-synthetic defect exchange (PSDE) as an alternative approach to introduce amino functionalities at missing-cluster defective sites in formic acid modulated UiO-66. Both pyridine-containing (picolinic acid and nicotinic acid) and aniline-containing (3-aminobenzoic acid and anthranilic acid) monocarboxylates were integrated within defective UiO-66 with this method. Non-defective UiO-66 modified with linkers bearing the same amino groups (2,5-pyridinedicarboxylic acid and 2-aminoterephthalic acid) were prepared by classical post-synthetic ligand exchange (PSE), in order to compare the effect of introducing functionalities at defective sites versus installing them on the backbone. PSDE reduces the porosity of defective UiO-66, but improves both the CO₂ uptake and the CO₂/N₂ selectivity, whereas PSE has no effect on the porosity of non-defective UiO-66, improving the CO₂ uptake but leaving selectivity unchanged. Modification of defective UiO-66 with benzoic acid reveals that pore size reduction is the main factor responsible for the observed uptake improvement, whereas the presence of nitrogen atoms in the pores seems to be beneficial for increasing selectivity.