A zirconium metal–organic framework with UiO-66 topology was synthesized using a 1,4-naphthalenedicarboxylic acid (NDC) linker (UiO-66-NDC). From synchrotron powder X-ray diffraction (PXRD), we found that the naphthalene rings of the NDC linker are out of (a,c)-plane equilibrium by 30°, similar to the situation found by single crystal XRD for the benzene rings in UiO-67 (Cryst. Growth Des. 2014, 14, 5370). Different fractions of the benzene-carboxylic (BC) acid modulator versus NDC were used to tune structural properties of the final product. The modulator increases both the crystal size and the surface area of the product, but reduces its thermal stability owing to insertion of defects: missing linkers and missing Zr6(OH)4O4 clusters. This study proves that the defect density (fraction of BC incorporation) can be tuned in UiO-66-NDC materials up to almost 50%. At that stage, the crystal is characterized also by a high density of missing Zr6(OH)4O4 inorganic cornerstones. Notwithstanding such structural defectivity, even the most defective material is stable after thermal activation at 200 °C (able to fully remove the solvent) and in water conditions, opening possibilities for application in the fields of catalysis and molecule sorption.